[1] "ofn"      "-oTOV-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/OV-TP/20141012/OV-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/19783384/transformed.cor.cli.txt"

nPatients in clinical file=596, in cluster file=579, common to both=579
[1]  82 579
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              168               411 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              168               411 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              221               358 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              221               358 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              186               393 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              186               393 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              155               424 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              155               424 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              160               419 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              160               419 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              275               304 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              275               304 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               60               519 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               60               519 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               547 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               547 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              199               380 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              199               380 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               60               519 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               60               519 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              170               409 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              170               409 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               97               482 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               97               482 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              181               398 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              181               398 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              203               376 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              203               376 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              119               460 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              119               460 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              242               337 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              242               337 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               92               487 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               92               487 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               45               534 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               45               534 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               188                391 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               188                391 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               111                468 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               111                468 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                77                502 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                77                502 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               115                464 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               115                464 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               255                324 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               255                324 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               177                402 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               177                402 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                60                519 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                60                519 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                59                520 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                59                520 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                40                539 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                40                539 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                520 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                520 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                548 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                548 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                557 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                557 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                532 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                532 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               120                459 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               120                459 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                72                507 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                72                507 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               171                408 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               171                408 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               161                418 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               161                418 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               289                290 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               289                290 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               328                251 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               328                251 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               109                470 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               109                470 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                555 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                555 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               78               501 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               78               501 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              108               471 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              108               471 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               65               514 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               65               514 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               43               536 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               43               536 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               53               526 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               53               526 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               520 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               520 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               95               484 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               95               484 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               536 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               536 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              316               263 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              316               263 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              362               217 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              362               217 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              133               446 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              133               446 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              223               356 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              223               356 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              165               414 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              165               414 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              242               337 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              242               337 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              121               458 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              121               458 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               498 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               498 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              277               302 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              277               302 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               90               489 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               90               489 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              262               317 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              262               317 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              286               293 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              286               293 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                97                482 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                97                482 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                455 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                455 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               198                381 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               198                381 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                431 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                431 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                79                500 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                79                500 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               105                474 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               105                474 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               310                269 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               310                269 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               215                364 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               215                364 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               280                299 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               280                299 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               334                245 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               334                245 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               413                166 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               413                166 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               478                101 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               478                101 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               383                196 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               383                196 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               235                344 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               235                344 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               293                286 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               293                286 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               185                394 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               185                394 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               178                401 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               178                401 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                50                529 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                50                529 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                547 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                547 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               199                380 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               199                380 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               430                149 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               430                149 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              325               254 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              325               254 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              280               299 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              280               299 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "MIR_CNMF"                    "MIR_CHIERARCHICAL"          
 [5] "CN_CNMF"                     "METHLYATION_CNMF"           
 [7] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [9] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[11] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[13] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 14 rows and 579 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIR_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 579 columns, 0 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "MIR_CNMF"                    "MIR_CHIERARCHICAL"          
 [5] "CN_CNMF"                     "METHLYATION_CNMF"           
 [7] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [9] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[11] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[13] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=10, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       51     72     38
  1P GAIN WILD-TYPE    164    144     88
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              51               164
  CLUS_2              72               144
  CLUS_3              38                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       93     48     20
  1P GAIN WILD-TYPE    217    110     69
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              93               217
  CLUS_2              48               110
  CLUS_3              20                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       53     38     68
  1P GAIN WILD-TYPE    106    126    164
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              53               106
  CLUS_2              38               126
  CLUS_3              68               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1P GAIN MUTATED       29      13     14     29      9     20     11     11
  1P GAIN WILD-TYPE     56      44     44     53     25     55     23     25
                   vv
clus                CLUS_8 CLUS_9
  1P GAIN MUTATED       14      9
  1P GAIN WILD-TYPE     38     33
D1V4, multiclass
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               29                56
  CLUS_10              13                44
  CLUS_2               14                44
  CLUS_3               29                53
  CLUS_4                9                25
  CLUS_5               20                55
  CLUS_6               11                23
  CLUS_7               11                25
  CLUS_8               14                38
  CLUS_9                9                33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       37     52     79
  1P GAIN WILD-TYPE    134    154    123
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              37               134
  CLUS_2              52               154
  CLUS_3              79               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
  1P GAIN MUTATED       56     42     67
  1P GAIN WILD-TYPE    116    133    154
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              56               116
  CLUS_2              42               133
  CLUS_3              67               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
  1P GAIN MUTATED       33     56     24
  1P GAIN WILD-TYPE    113    133     52
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              33               113
  CLUS_2              56               133
  CLUS_3              24                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED       39     17     15     42
  1P GAIN WILD-TYPE    104     37     45    112
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              39               104
  CLUS_2              17                37
  CLUS_3              15                45
  CLUS_4              42               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       22     38     31
  1P GAIN WILD-TYPE     57     70     82
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              22                57
  CLUS_2              38                70
  CLUS_3              31                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       42     21     28
  1P GAIN WILD-TYPE    104     38     67
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              42               104
  CLUS_2              21                38
  CLUS_3              28                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       31     63     45
  1P GAIN WILD-TYPE     90    119     99
D1V11, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              31                90
  CLUS_2              63               119
  CLUS_3              45                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED       29     20     56     34
  1P GAIN WILD-TYPE     76     51    109     72
D1V12, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              29                76
  CLUS_2              20                51
  CLUS_3              56               109
  CLUS_4              34                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"
D1V13, binary
                   cls
clus                0 1
  1P GAIN MUTATED   7 3
  1P GAIN WILD-TYPE 5 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7    3
  1P GAIN WILD-TYPE    5    7
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7                 5
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P GAIN MUTATED        3      0      0      3      3      1
  1P GAIN WILD-TYPE      3      2      2      3      1      1
D1V14, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               3                 3
  CLUS_5               3                 1
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       84     81     45
  1Q GAIN WILD-TYPE    131    135     81
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              84               131
  CLUS_2              81               135
  CLUS_3              45                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED      118     53     39
  1Q GAIN WILD-TYPE    192    105     50
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1             118               192
  CLUS_2              53               105
  CLUS_3              39                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       64     59     85
  1Q GAIN WILD-TYPE     95    105    147
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              64                95
  CLUS_2              59               105
  CLUS_3              85               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1Q GAIN MUTATED       32      19     22     31      8     33     12     15
  1Q GAIN WILD-TYPE     53      38     36     51     26     42     22     21
                   vv
clus                CLUS_8 CLUS_9
  1Q GAIN MUTATED       26     10
  1Q GAIN WILD-TYPE     26     32
D2V4, multiclass
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               32                53
  CLUS_10              19                38
  CLUS_2               22                36
  CLUS_3               31                51
  CLUS_4                8                26
  CLUS_5               33                42
  CLUS_6               12                22
  CLUS_7               15                21
  CLUS_8               26                26
  CLUS_9               10                32
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       56     55    110
  1Q GAIN WILD-TYPE    115    151     92
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              56               115
  CLUS_2              55               151
  CLUS_3             110                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       82     57     78
  1Q GAIN WILD-TYPE     90    118    143
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              82                90
  CLUS_2              57               118
  CLUS_3              78               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
  1Q GAIN MUTATED       53     78     25
  1Q GAIN WILD-TYPE     93    111     51
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              53                93
  CLUS_2              78               111
  CLUS_3              25                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED       53     22     19     62
  1Q GAIN WILD-TYPE     90     32     41     92
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              53                90
  CLUS_2              22                32
  CLUS_3              19                41
  CLUS_4              62                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
  1Q GAIN MUTATED       27     53     39
  1Q GAIN WILD-TYPE     52     55     74
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              27                52
  CLUS_2              53                55
  CLUS_3              39                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       52     31     36
  1Q GAIN WILD-TYPE     94     28     59
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              52                94
  CLUS_2              31                28
  CLUS_3              36                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       40     76     61
  1Q GAIN WILD-TYPE     81    106     83
D2V11, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              40                81
  CLUS_2              76               106
  CLUS_3              61                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED       31     30     69     47
  1Q GAIN WILD-TYPE     74     41     96     59
D2V12, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              31                74
  CLUS_2              30                41
  CLUS_3              69                96
  CLUS_4              47                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"
D2V13, binary
                   cls
clus                0 1
  1Q GAIN MUTATED   8 3
  1Q GAIN WILD-TYPE 4 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    3
  1Q GAIN WILD-TYPE    4    7
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8                 4
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q GAIN MUTATED        4      0      0      4      2      1
  1Q GAIN WILD-TYPE      2      2      2      2      2      1
D2V14, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               4                 2
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       93     45     36
  2P GAIN WILD-TYPE    122    171     90
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              93               122
  CLUS_2              45               171
  CLUS_3              36                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       77     48     49
  2P GAIN WILD-TYPE    233    110     40
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              77               233
  CLUS_2              48               110
  CLUS_3              49                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       50     49     75
  2P GAIN WILD-TYPE    109    115    157
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              50               109
  CLUS_2              49               115
  CLUS_3              75               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2P GAIN MUTATED       21      16     22     21     10     20     17      9
  2P GAIN WILD-TYPE     64      41     36     61     24     55     17     27
                   vv
clus                CLUS_8 CLUS_9
  2P GAIN MUTATED       30      8
  2P GAIN WILD-TYPE     22     34
D3V4, multiclass
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               21                64
  CLUS_10              16                41
  CLUS_2               22                36
  CLUS_3               21                61
  CLUS_4               10                24
  CLUS_5               20                55
  CLUS_6               17                17
  CLUS_7                9                27
  CLUS_8               30                22
  CLUS_9                8                34
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       37     47    102
  2P GAIN WILD-TYPE    134    159    100
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              37               134
  CLUS_2              47               159
  CLUS_3             102               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
  2P GAIN MUTATED       83     44     52
  2P GAIN WILD-TYPE     89    131    169
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              83                89
  CLUS_2              44               131
  CLUS_3              52               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
  2P GAIN MUTATED       46     74     14
  2P GAIN WILD-TYPE    100    115     62
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              46               100
  CLUS_2              74               115
  CLUS_3              14                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       46     13     23     52
  2P GAIN WILD-TYPE     97     41     37    102
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              46                97
  CLUS_2              13                41
  CLUS_3              23                37
  CLUS_4              52               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       13     54     39
  2P GAIN WILD-TYPE     66     54     74
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              13                66
  CLUS_2              54                54
  CLUS_3              39                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       33     37     36
  2P GAIN WILD-TYPE    113     22     59
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              33               113
  CLUS_2              37                22
  CLUS_3              36                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       41     56     48
  2P GAIN WILD-TYPE     80    126     96
D3V11, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              41                80
  CLUS_2              56               126
  CLUS_3              48                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED       23     27     63     32
  2P GAIN WILD-TYPE     82     44    102     74
D3V12, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              23                82
  CLUS_2              27                44
  CLUS_3              63               102
  CLUS_4              32                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"
D3V13, binary
                   cls
clus                0 1
  2P GAIN MUTATED   5 3
  2P GAIN WILD-TYPE 7 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    3
  2P GAIN WILD-TYPE    7    7
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2P GAIN MUTATED        2      0      0      2      3      1
  2P GAIN WILD-TYPE      4      2      2      4      1      1
D3V14, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                 4
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               3                 1
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       76     42     29
  2Q GAIN WILD-TYPE    139    174     97
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              76               139
  CLUS_2              42               174
  CLUS_3              29                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       70     36     41
  2Q GAIN WILD-TYPE    240    122     48
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              70               240
  CLUS_2              36               122
  CLUS_3              41                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       42     43     61
  2Q GAIN WILD-TYPE    117    121    171
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              42               117
  CLUS_2              43               121
  CLUS_3              61               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2Q GAIN MUTATED       16      12     18     18      9     20     15      6
  2Q GAIN WILD-TYPE     69      45     40     64     25     55     19     30
                   vv
clus                CLUS_8 CLUS_9
  2Q GAIN MUTATED       24      8
  2Q GAIN WILD-TYPE     28     34
D4V4, multiclass
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               16                69
  CLUS_10              12                45
  CLUS_2               18                40
  CLUS_3               18                64
  CLUS_4                9                25
  CLUS_5               20                55
  CLUS_6               15                19
  CLUS_7                6                30
  CLUS_8               24                28
  CLUS_9                8                34
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     40     84
  2Q GAIN WILD-TYPE    140    166    118
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              31               140
  CLUS_2              40               166
  CLUS_3              84               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
  2Q GAIN MUTATED       66     36     49
  2Q GAIN WILD-TYPE    106    139    172
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              66               106
  CLUS_2              36               139
  CLUS_3              49               172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       35     59     13
  2Q GAIN WILD-TYPE    111    130     63
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              35               111
  CLUS_2              59               130
  CLUS_3              13                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       37     12     17     41
  2Q GAIN WILD-TYPE    106     42     43    113
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              37               106
  CLUS_2              12                42
  CLUS_3              17                43
  CLUS_4              41               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
  2Q GAIN MUTATED       10     44     30
  2Q GAIN WILD-TYPE     69     64     83
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              10                69
  CLUS_2              44                64
  CLUS_3              30                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       29     29     26
  2Q GAIN WILD-TYPE    117     30     69
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              29               117
  CLUS_2              29                30
  CLUS_3              26                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       29     53     40
  2Q GAIN WILD-TYPE     92    129    104
D4V11, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              29                92
  CLUS_2              53               129
  CLUS_3              40               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED       16     23     55     28
  2Q GAIN WILD-TYPE     89     48    110     78
D4V12, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              16                89
  CLUS_2              23                48
  CLUS_3              55               110
  CLUS_4              28                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"
D4V13, binary
                   cls
clus                0 1
  2Q GAIN MUTATED   3 3
  2Q GAIN WILD-TYPE 9 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    3
  2Q GAIN WILD-TYPE    9    7
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q GAIN MUTATED        1      0      0      2      2      1
  2Q GAIN WILD-TYPE      5      2      2      4      2      1
D4V14, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       53     63     38
  3P GAIN WILD-TYPE    162    153     88
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              53               162
  CLUS_2              63               153
  CLUS_3              38                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       87     47     20
  3P GAIN WILD-TYPE    223    111     69
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              87               223
  CLUS_2              47               111
  CLUS_3              20                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       53     47     53
  3P GAIN WILD-TYPE    106    117    179
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              53               106
  CLUS_2              47               117
  CLUS_3              53               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3P GAIN MUTATED       24      21     19     20     11     21      8     11
  3P GAIN WILD-TYPE     61      36     39     62     23     54     26     25
                   vv
clus                CLUS_8 CLUS_9
  3P GAIN MUTATED        9      9
  3P GAIN WILD-TYPE     43     33
D5V4, multiclass
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               24                61
  CLUS_10              21                36
  CLUS_2               19                39
  CLUS_3               20                62
  CLUS_4               11                23
  CLUS_5               21                54
  CLUS_6                8                26
  CLUS_7               11                25
  CLUS_8                9                43
  CLUS_9                9                33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       38     51     71
  3P GAIN WILD-TYPE    133    155    131
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              38               133
  CLUS_2              51               155
  CLUS_3              71               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
  3P GAIN MUTATED       50     45     62
  3P GAIN WILD-TYPE    122    130    159
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              50               122
  CLUS_2              45               130
  CLUS_3              62               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
  3P GAIN MUTATED       40     52     23
  3P GAIN WILD-TYPE    106    137     53
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              40               106
  CLUS_2              52               137
  CLUS_3              23                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED       45     15     15     40
  3P GAIN WILD-TYPE     98     39     45    114
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              45                98
  CLUS_2              15                39
  CLUS_3              15                45
  CLUS_4              40               114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       20     29     37
  3P GAIN WILD-TYPE     59     79     76
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              20                59
  CLUS_2              29                79
  CLUS_3              37                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       41     16     29
  3P GAIN WILD-TYPE    105     43     66
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              41               105
  CLUS_2              16                43
  CLUS_3              29                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       34     50     41
  3P GAIN WILD-TYPE     87    132    103
D5V11, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              34                87
  CLUS_2              50               132
  CLUS_3              41               103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED       26     19     48     32
  3P GAIN WILD-TYPE     79     52    117     74
D5V12, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              26                79
  CLUS_2              19                52
  CLUS_3              48               117
  CLUS_4              32                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"
D5V13, binary
                   cls
clus                0 1
  3P GAIN MUTATED   3 3
  3P GAIN WILD-TYPE 9 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    3
  3P GAIN WILD-TYPE    9    7
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P GAIN MUTATED        2      0      0      2      2      0
  3P GAIN WILD-TYPE      4      2      2      4      2      2
D5V14, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                 4
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               2                 2
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED      104    101     59
  3Q GAIN WILD-TYPE    111    115     67
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1             104               111
  CLUS_2             101               115
  CLUS_3              59                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED      144     76     44
  3Q GAIN WILD-TYPE    166     82     45
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1             144               166
  CLUS_2              76                82
  CLUS_3              44                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       77     84    102
  3Q GAIN WILD-TYPE     82     80    130
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              77                82
  CLUS_2              84                80
  CLUS_3             102               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3Q GAIN MUTATED       34      30     28     34     17     38     16     22
  3Q GAIN WILD-TYPE     51      27     30     48     17     37     18     14
                   vv
clus                CLUS_8 CLUS_9
  3Q GAIN MUTATED       28     16
  3Q GAIN WILD-TYPE     24     26
D6V4, multiclass
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               34                51
  CLUS_10              30                27
  CLUS_2               28                30
  CLUS_3               34                48
  CLUS_4               17                17
  CLUS_5               38                37
  CLUS_6               16                18
  CLUS_7               22                14
  CLUS_8               28                24
  CLUS_9               16                26
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       58     90    127
  3Q GAIN WILD-TYPE    113    116     75
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              58               113
  CLUS_2              90               116
  CLUS_3             127                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       96     72     99
  3Q GAIN WILD-TYPE     76    103    122
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              96                76
  CLUS_2              72               103
  CLUS_3              99               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
  3Q GAIN MUTATED       68     90     36
  3Q GAIN WILD-TYPE     78     99     40
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              68                78
  CLUS_2              90                99
  CLUS_3              36                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       71     21     34     68
  3Q GAIN WILD-TYPE     72     33     26     86
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              71                72
  CLUS_2              21                33
  CLUS_3              34                26
  CLUS_4              68                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       36     60     52
  3Q GAIN WILD-TYPE     43     48     61
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              36                43
  CLUS_2              60                48
  CLUS_3              52                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     33     47
  3Q GAIN WILD-TYPE     78     26     48
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              68                78
  CLUS_2              33                26
  CLUS_3              47                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       62     77     71
  3Q GAIN WILD-TYPE     59    105     73
D6V11, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              62                59
  CLUS_2              77               105
  CLUS_3              71                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       38     35     83     54
  3Q GAIN WILD-TYPE     67     36     82     52
D6V12, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              38                67
  CLUS_2              35                36
  CLUS_3              83                82
  CLUS_4              54                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                   cls
clus                0 1
  3Q GAIN MUTATED   4 4
  3Q GAIN WILD-TYPE 8 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    4
  3Q GAIN WILD-TYPE    8    6
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               4                 6
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q GAIN MUTATED        3      0      0      3      2      0
  3Q GAIN WILD-TYPE      3      2      2      3      2      2
D6V14, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               3                 3
  CLUS_5               2                 2
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       22     17     17
  4P GAIN WILD-TYPE    193    199    109
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              22               193
  CLUS_2              17               199
  CLUS_3              17               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       25     21     10
  4P GAIN WILD-TYPE    285    137     79
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              25               285
  CLUS_2              21               137
  CLUS_3              10                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        7     16     33
  4P GAIN WILD-TYPE    152    148    199
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               7               152
  CLUS_2              16               148
  CLUS_3              33               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4P GAIN MUTATED        5       4      2      5      3     12      7      4
  4P GAIN WILD-TYPE     80      53     56     77     31     63     27     32
                   vv
clus                CLUS_8 CLUS_9
  4P GAIN MUTATED        8      6
  4P GAIN WILD-TYPE     44     36
D7V4, multiclass
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1                5                80
  CLUS_10               4                53
  CLUS_2                2                56
  CLUS_3                5                77
  CLUS_4                3                31
  CLUS_5               12                63
  CLUS_6                7                27
  CLUS_7                4                32
  CLUS_8                8                44
  CLUS_9                6                36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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        9     23     28
  4P GAIN WILD-TYPE    162    183    174
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               9               162
  CLUS_2              23               183
  CLUS_3              28               174
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       24     16     17
  4P GAIN WILD-TYPE    148    159    204
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              24               148
  CLUS_2              16               159
  CLUS_3              17               204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       13     24      9
  4P GAIN WILD-TYPE    133    165     67
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              13               133
  CLUS_2              24               165
  CLUS_3               9                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED       13      8      9     16
  4P GAIN WILD-TYPE    130     46     51    138
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              13               130
  CLUS_2               8                46
  CLUS_3               9                51
  CLUS_4              16               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        8     15     15
  4P GAIN WILD-TYPE     71     93     98
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               8                71
  CLUS_2              15                93
  CLUS_3              15                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       15      9     14
  4P GAIN WILD-TYPE    131     50     81
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              15               131
  CLUS_2               9                50
  CLUS_3              14                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       18     20     13
  4P GAIN WILD-TYPE    103    162    131
D7V11, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              18               103
  CLUS_2              20               162
  CLUS_3              13               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        8     13     24      6
  4P GAIN WILD-TYPE     97     58    141    100
D7V12, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               8                97
  CLUS_2              13                58
  CLUS_3              24               141
  CLUS_4               6               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"
D7V13, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 10  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   10    9
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P GAIN MUTATED        1      0      0      0      1      1
  4P GAIN WILD-TYPE      5      2      2      6      3      1
D7V14, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               0                 6
  CLUS_5               1                 3
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED       14      9      8
  4Q GAIN WILD-TYPE    201    207    118
D8V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1              14               201
  CLUS_2               9               207
  CLUS_3               8               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
  4Q GAIN MUTATED       19      7      5
  4Q GAIN WILD-TYPE    291    151     84
D8V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1              19               291
  CLUS_2               7               151
  CLUS_3               5                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        5      9     17
  4Q GAIN WILD-TYPE    154    155    215
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               5               154
  CLUS_2               9               155
  CLUS_3              17               215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4Q GAIN MUTATED        2       3      0      3      1      6      4      3
  4Q GAIN WILD-TYPE     83      54     58     79     33     69     30     33
                   vv
clus                CLUS_8 CLUS_9
  4Q GAIN MUTATED        6      3
  4Q GAIN WILD-TYPE     46     39
D8V4, multiclass
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1                2                83
  CLUS_10               3                54
  CLUS_2                0                58
  CLUS_3                3                79
  CLUS_4                1                33
  CLUS_5                6                69
  CLUS_6                4                30
  CLUS_7                3                33
  CLUS_8                6                46
  CLUS_9                3                39
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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        2     15     15
  4Q GAIN WILD-TYPE    169    191    187
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               169
  CLUS_2              15               191
  CLUS_3              15               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED       17      8      6
  4Q GAIN WILD-TYPE    155    167    215
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1              17               155
  CLUS_2               8               167
  CLUS_3               6               215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        7     13      5
  4Q GAIN WILD-TYPE    139    176     71
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               7               139
  CLUS_2              13               176
  CLUS_3               5                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9      4      8      4
  4Q GAIN WILD-TYPE    134     50     52    150
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               9               134
  CLUS_2               4                50
  CLUS_3               8                52
  CLUS_4               4               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      9      7
  4Q GAIN WILD-TYPE     75     99    106
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4                75
  CLUS_2               9                99
  CLUS_3               7               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        9      6      5
  4Q GAIN WILD-TYPE    137     53     90
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               9               137
  CLUS_2               6                53
  CLUS_3               5                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED       10     12      5
  4Q GAIN WILD-TYPE    111    170    139
D8V11, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1              10               111
  CLUS_2              12               170
  CLUS_3               5               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
  4Q GAIN MUTATED        3      6     15      3
  4Q GAIN WILD-TYPE    102     65    150    103
D8V12, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               102
  CLUS_2               6                65
  CLUS_3              15               150
  CLUS_4               3               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"
D8V13, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  0
  4Q GAIN WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    0
  4Q GAIN WILD-TYPE   12   10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q GAIN MUTATED        0      0      0      0      0      0
  4Q GAIN WILD-TYPE      6      2      2      6      4      2
D8V14, multiclass

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       71     71     48
  5P GAIN WILD-TYPE    144    145     78
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              71               144
  CLUS_2              71               145
  CLUS_3              48                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED      109     54     27
  5P GAIN WILD-TYPE    201    104     62
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1             109               201
  CLUS_2              54               104
  CLUS_3              27                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       57     54     79
  5P GAIN WILD-TYPE    102    110    153
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              57               102
  CLUS_2              54               110
  CLUS_3              79               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5P GAIN MUTATED       26      16     21     29     11     33     13     10
  5P GAIN WILD-TYPE     59      41     37     53     23     42     21     26
                   vv
clus                CLUS_8 CLUS_9
  5P GAIN MUTATED       18     13
  5P GAIN WILD-TYPE     34     29
D9V4, multiclass
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               26                59
  CLUS_10              16                41
  CLUS_2               21                37
  CLUS_3               29                53
  CLUS_4               11                23
  CLUS_5               33                42
  CLUS_6               13                21
  CLUS_7               10                26
  CLUS_8               18                34
  CLUS_9               13                29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       39     77     83
  5P GAIN WILD-TYPE    132    129    119
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              39               132
  CLUS_2              77               129
  CLUS_3              83               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
  5P GAIN MUTATED       67     52     76
  5P GAIN WILD-TYPE    105    123    145
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              67               105
  CLUS_2              52               123
  CLUS_3              76               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
  5P GAIN MUTATED       56     60     25
  5P GAIN WILD-TYPE     90    129     51
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              56                90
  CLUS_2              60               129
  CLUS_3              25                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED       58     16     21     46
  5P GAIN WILD-TYPE     85     38     39    108
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              58                85
  CLUS_2              16                38
  CLUS_3              21                39
  CLUS_4              46               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
  5P GAIN MUTATED       30     35     34
  5P GAIN WILD-TYPE     49     73     79
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              30                49
  CLUS_2              35                73
  CLUS_3              34                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       54     15     30
  5P GAIN WILD-TYPE     92     44     65
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              54                92
  CLUS_2              15                44
  CLUS_3              30                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       42     71     42
  5P GAIN WILD-TYPE     79    111    102
D9V11, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              42                79
  CLUS_2              71               111
  CLUS_3              42               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED       35     22     64     34
  5P GAIN WILD-TYPE     70     49    101     72
D9V12, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              35                70
  CLUS_2              22                49
  CLUS_3              64               101
  CLUS_4              34                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"
D9V13, binary
                   cls
clus                0 1
  5P GAIN MUTATED   4 5
  5P GAIN WILD-TYPE 8 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    5
  5P GAIN WILD-TYPE    8    5
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               5                 5
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P GAIN MUTATED        2      1      0      1      3      2
  5P GAIN WILD-TYPE      4      1      2      5      1      0
D9V14, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 4
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               3                 1
  CLUS_6               2                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       15     23     19
  5Q GAIN WILD-TYPE    200    193    107
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              15               200
  CLUS_2              23               193
  CLUS_3              19               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
  5Q GAIN MUTATED       28     22      7
  5Q GAIN WILD-TYPE    282    136     82
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              28               282
  CLUS_2              22               136
  CLUS_3               7                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       18     15     24
  5Q GAIN WILD-TYPE    141    149    208
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              18               141
  CLUS_2              15               149
  CLUS_3              24               208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5Q GAIN MUTATED        8       3      8     10      3      8      5      3
  5Q GAIN WILD-TYPE     77      54     50     72     31     67     29     33
                   vv
clus                CLUS_8 CLUS_9
  5Q GAIN MUTATED        4      5
  5Q GAIN WILD-TYPE     48     37
D10V4, multiclass
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1                8                77
  CLUS_10               3                54
  CLUS_2                8                50
  CLUS_3               10                72
  CLUS_4                3                31
  CLUS_5                8                67
  CLUS_6                5                29
  CLUS_7                3                33
  CLUS_8                4                48
  CLUS_9                5                37
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     20     23
  5Q GAIN WILD-TYPE    154    186    179
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              17               154
  CLUS_2              20               186
  CLUS_3              23               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       15     22     22
  5Q GAIN WILD-TYPE    157    153    199
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              15               157
  CLUS_2              22               153
  CLUS_3              22               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       14     18     10
  5Q GAIN WILD-TYPE    132    171     66
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              14               132
  CLUS_2              18               171
  CLUS_3              10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED       17      5      7     13
  5Q GAIN WILD-TYPE    126     49     53    141
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              17               126
  CLUS_2               5                49
  CLUS_3               7                53
  CLUS_4              13               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        8      7     11
  5Q GAIN WILD-TYPE     71    101    102
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               8                71
  CLUS_2               7               101
  CLUS_3              11               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       11      3     12
  5Q GAIN WILD-TYPE    135     56     83
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              11               135
  CLUS_2               3                56
  CLUS_3              12                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       12     21     10
  5Q GAIN WILD-TYPE    109    161    134
D10V11, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              12               109
  CLUS_2              21               161
  CLUS_3              10               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
  5Q GAIN MUTATED       12      6     17      8
  5Q GAIN WILD-TYPE     93     65    148     98
D10V12, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              12                93
  CLUS_2               6                65
  CLUS_3              17               148
  CLUS_4               8                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"
D10V13, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    2  0
  5Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    0
  5Q GAIN WILD-TYPE   10   10
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q GAIN MUTATED        0      0      0      0      0      2
  5Q GAIN WILD-TYPE      6      2      2      6      4      0
D10V14, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                20 
       TCGA-04-1652        TCGA-09-2050        TCGA-09-2054        TCGA-13-0908 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-23-2077        TCGA-24-1928        TCGA-24-2036        TCGA-24-2289 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-24-2290        TCGA-24-2297        TCGA-25-2399        TCGA-25-2400 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-25-2404        TCGA-57-1994        TCGA-59-2363        TCGA-61-1918 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-61-2088        TCGA-61-2098        TCGA-61-2109        TCGA-61-2111 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       65     57     40
  6P GAIN WILD-TYPE    150    159     86
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              65               150
  CLUS_2              57               159
  CLUS_3              40                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       79     44     39
  6P GAIN WILD-TYPE    231    114     50
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              79               231
  CLUS_2              44               114
  CLUS_3              39                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       44     49     68
  6P GAIN WILD-TYPE    115    115    164
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              44               115
  CLUS_2              49               115
  CLUS_3              68               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6P GAIN MUTATED       20      13     14     20     11     28     11     13
  6P GAIN WILD-TYPE     65      44     44     62     23     47     23     23
                   vv
clus                CLUS_8 CLUS_9
  6P GAIN MUTATED       25      6
  6P GAIN WILD-TYPE     27     36
D11V4, multiclass
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               20                65
  CLUS_10              13                44
  CLUS_2               14                44
  CLUS_3               20                62
  CLUS_4               11                23
  CLUS_5               28                47
  CLUS_6               11                23
  CLUS_7               13                23
  CLUS_8               25                27
  CLUS_9                6                36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       29     56     85
  6P GAIN WILD-TYPE    142    150    117
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              29               142
  CLUS_2              56               150
  CLUS_3              85               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
  6P GAIN MUTATED       72     39     55
  6P GAIN WILD-TYPE    100    136    166
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              72               100
  CLUS_2              39               136
  CLUS_3              55               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
  6P GAIN MUTATED       43     54     21
  6P GAIN WILD-TYPE    103    135     55
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              43               103
  CLUS_2              54               135
  CLUS_3              21                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED       40     13     21     44
  6P GAIN WILD-TYPE    103     41     39    110
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              40               103
  CLUS_2              13                41
  CLUS_3              21                39
  CLUS_4              44               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
  6P GAIN MUTATED       20     42     36
  6P GAIN WILD-TYPE     59     66     77
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              20                59
  CLUS_2              42                66
  CLUS_3              36                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       36     31     31
  6P GAIN WILD-TYPE    110     28     64
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              36               110
  CLUS_2              31                28
  CLUS_3              31                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       42     49     44
  6P GAIN WILD-TYPE     79    133    100
D11V11, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              42                79
  CLUS_2              49               133
  CLUS_3              44               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED       28     31     48     28
  6P GAIN WILD-TYPE     77     40    117     78
D11V12, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              28                77
  CLUS_2              31                40
  CLUS_3              48               117
  CLUS_4              28                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"
D11V13, binary
                   cls
clus                0 1
  6P GAIN MUTATED   6 3
  6P GAIN WILD-TYPE 6 7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    3
  6P GAIN WILD-TYPE    6    7
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               6                 6
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P GAIN MUTATED        4      1      0      2      1      1
  6P GAIN WILD-TYPE      2      1      2      4      3      1
D11V14, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               1                 3
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       36     33     24
  6Q GAIN WILD-TYPE    179    183    102
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              36               179
  CLUS_2              33               183
  CLUS_3              24               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       46     24     23
  6Q GAIN WILD-TYPE    264    134     66
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              46               264
  CLUS_2              24               134
  CLUS_3              23                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       26     25     41
  6Q GAIN WILD-TYPE    133    139    191
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              26               133
  CLUS_2              25               139
  CLUS_3              41               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6Q GAIN MUTATED       11       5      9     14      7      9     10      8
  6Q GAIN WILD-TYPE     74      52     49     68     27     66     24     28
                   vv
clus                CLUS_8 CLUS_9
  6Q GAIN MUTATED       16      3
  6Q GAIN WILD-TYPE     36     39
D12V4, multiclass
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               11                74
  CLUS_10               5                52
  CLUS_2                9                49
  CLUS_3               14                68
  CLUS_4                7                27
  CLUS_5                9                66
  CLUS_6               10                24
  CLUS_7                8                28
  CLUS_8               16                36
  CLUS_9                3                39
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       12     30     55
  6Q GAIN WILD-TYPE    159    176    147
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              12               159
  CLUS_2              30               176
  CLUS_3              55               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
  6Q GAIN MUTATED       48     16     32
  6Q GAIN WILD-TYPE    124    159    189
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              48               124
  CLUS_2              16               159
  CLUS_3              32               189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       21     31     13
  6Q GAIN WILD-TYPE    125    158     63
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              21               125
  CLUS_2              31               158
  CLUS_3              13                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       22      7     13     23
  6Q GAIN WILD-TYPE    121     47     47    131
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              22               121
  CLUS_2               7                47
  CLUS_3              13                47
  CLUS_4              23               131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       10     26     19
  6Q GAIN WILD-TYPE     69     82     94
D12V9, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              10                69
  CLUS_2              26                82
  CLUS_3              19                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       23     18     14
  6Q GAIN WILD-TYPE    123     41     81
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              23               123
  CLUS_2              18                41
  CLUS_3              14                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       28     32     21
  6Q GAIN WILD-TYPE     93    150    123
D12V11, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              28                93
  CLUS_2              32               150
  CLUS_3              21               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 CLUS_4
  6Q GAIN MUTATED       15     19     35     12
  6Q GAIN WILD-TYPE     90     52    130     94
D12V12, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              15                90
  CLUS_2              19                52
  CLUS_3              35               130
  CLUS_4              12                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"
D12V13, binary
                   cls
clus                0 1
  6Q GAIN MUTATED   5 2
  6Q GAIN WILD-TYPE 7 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    2
  6Q GAIN WILD-TYPE    7    8
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q GAIN MUTATED        3      0      0      1      2      1
  6Q GAIN WILD-TYPE      3      2      2      5      2      1
D12V14, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       70     63     43
  7P GAIN WILD-TYPE    145    153     83
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              70               145
  CLUS_2              63               153
  CLUS_3              43                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       99     45     32
  7P GAIN WILD-TYPE    211    113     57
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              99               211
  CLUS_2              45               113
  CLUS_3              32                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       52     41     82
  7P GAIN WILD-TYPE    107    123    150
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              52               107
  CLUS_2              41               123
  CLUS_3              82               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7P GAIN MUTATED       29      17     18     23     10     26     17      9
  7P GAIN WILD-TYPE     56      40     40     59     24     49     17     27
                   vv
clus                CLUS_8 CLUS_9
  7P GAIN MUTATED       20      6
  7P GAIN WILD-TYPE     32     36
D13V4, multiclass
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               29                56
  CLUS_10              17                40
  CLUS_2               18                40
  CLUS_3               23                59
  CLUS_4               10                24
  CLUS_5               26                49
  CLUS_6               17                17
  CLUS_7                9                27
  CLUS_8               20                32
  CLUS_9                6                36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       43     44     94
  7P GAIN WILD-TYPE    128    162    108
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              43               128
  CLUS_2              44               162
  CLUS_3              94               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
  7P GAIN MUTATED       75     41     63
  7P GAIN WILD-TYPE     97    134    158
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              75                97
  CLUS_2              41               134
  CLUS_3              63               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
  7P GAIN MUTATED       44     60     22
  7P GAIN WILD-TYPE    102    129     54
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              44               102
  CLUS_2              60               129
  CLUS_3              22                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       42     17     12     55
  7P GAIN WILD-TYPE    101     37     48     99
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              42               101
  CLUS_2              17                37
  CLUS_3              12                48
  CLUS_4              55                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
  7P GAIN MUTATED       21     29     33
  7P GAIN WILD-TYPE     58     79     80
D13V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              21                58
  CLUS_2              29                79
  CLUS_3              33                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       38     17     28
  7P GAIN WILD-TYPE    108     42     67
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              38               108
  CLUS_2              17                42
  CLUS_3              28                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       36     57     45
  7P GAIN WILD-TYPE     85    125     99
D13V11, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              36                85
  CLUS_2              57               125
  CLUS_3              45                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       24     20     60     34
  7P GAIN WILD-TYPE     81     51    105     72
D13V12, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              24                81
  CLUS_2              20                51
  CLUS_3              60               105
  CLUS_4              34                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"
D13V13, binary
                   cls
clus                0 1
  7P GAIN MUTATED   5 4
  7P GAIN WILD-TYPE 7 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    4
  7P GAIN WILD-TYPE    7    6
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               4                 6
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P GAIN MUTATED        4      1      0      2      1      1
  7P GAIN WILD-TYPE      2      1      2      4      3      1
D13V14, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               1                 3
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       79     75     40
  7Q GAIN WILD-TYPE    136    141     86
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              79               136
  CLUS_2              75               141
  CLUS_3              40                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED      118     44     32
  7Q GAIN WILD-TYPE    192    114     57
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1             118               192
  CLUS_2              44               114
  CLUS_3              32                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       60     49     83
  7Q GAIN WILD-TYPE     99    115    149
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              60                99
  CLUS_2              49               115
  CLUS_3              83               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7Q GAIN MUTATED       32      21     20     26     12     26     18     10
  7Q GAIN WILD-TYPE     53      36     38     56     22     49     16     26
                   vv
clus                CLUS_8 CLUS_9
  7Q GAIN MUTATED       18      9
  7Q GAIN WILD-TYPE     34     33
D14V4, multiclass
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               32                53
  CLUS_10              21                36
  CLUS_2               20                38
  CLUS_3               26                56
  CLUS_4               12                22
  CLUS_5               26                49
  CLUS_6               18                16
  CLUS_7               10                26
  CLUS_8               18                34
  CLUS_9                9                33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       46     57    100
  7Q GAIN WILD-TYPE    125    149    102
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              46               125
  CLUS_2              57               149
  CLUS_3             100               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       76     45     77
  7Q GAIN WILD-TYPE     96    130    144
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              76                96
  CLUS_2              45               130
  CLUS_3              77               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
  7Q GAIN MUTATED       47     69     23
  7Q GAIN WILD-TYPE     99    120     53
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              47                99
  CLUS_2              69               120
  CLUS_3              23                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       47     17     15     60
  7Q GAIN WILD-TYPE     96     37     45     94
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              47                96
  CLUS_2              17                37
  CLUS_3              15                45
  CLUS_4              60                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
  7Q GAIN MUTATED       22     31     37
  7Q GAIN WILD-TYPE     57     77     76
D14V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              22                57
  CLUS_2              31                77
  CLUS_3              37                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       44     17     29
  7Q GAIN WILD-TYPE    102     42     66
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              44               102
  CLUS_2              17                42
  CLUS_3              29                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       33     68     53
  7Q GAIN WILD-TYPE     88    114     91
D14V11, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              33                88
  CLUS_2              68               114
  CLUS_3              53                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       32     23     58     41
  7Q GAIN WILD-TYPE     73     48    107     65
D14V12, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              32                73
  CLUS_2              23                48
  CLUS_3              58               107
  CLUS_4              41                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"
D14V13, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   4 2
  7Q GAIN WILD-TYPE 8 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    2
  7Q GAIN WILD-TYPE    8    8
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 8
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q GAIN MUTATED        4      0      0      1      1      0
  7Q GAIN WILD-TYPE      2      2      2      5      3      2
D14V14, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               1                 3
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       44     37     35
  8P GAIN WILD-TYPE    171    179     91
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              44               171
  CLUS_2              37               179
  CLUS_3              35                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       49     45     22
  8P GAIN WILD-TYPE    261    113     67
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              49               261
  CLUS_2              45               113
  CLUS_3              22                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       39     33     44
  8P GAIN WILD-TYPE    120    131    188
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              39               120
  CLUS_2              33               131
  CLUS_3              44               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P GAIN MUTATED       21      11     10     12      7     18     11      4
  8P GAIN WILD-TYPE     64      46     48     70     27     57     23     32
                   vv
clus                CLUS_8 CLUS_9
  8P GAIN MUTATED       11     11
  8P GAIN WILD-TYPE     41     31
D15V4, multiclass
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               21                64
  CLUS_10              11                46
  CLUS_2               10                48
  CLUS_3               12                70
  CLUS_4                7                27
  CLUS_5               18                57
  CLUS_6               11                23
  CLUS_7                4                32
  CLUS_8               11                41
  CLUS_9               11                31
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       32     46     41
  8P GAIN WILD-TYPE    139    160    161
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              32               139
  CLUS_2              46               160
  CLUS_3              41               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
  8P GAIN MUTATED       34     39     44
  8P GAIN WILD-TYPE    138    136    177
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              34               138
  CLUS_2              39               136
  CLUS_3              44               177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       29     30     20
  8P GAIN WILD-TYPE    117    159     56
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              29               117
  CLUS_2              30               159
  CLUS_3              20                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED       31     14     10     24
  8P GAIN WILD-TYPE    112     40     50    130
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              31               112
  CLUS_2              14                40
  CLUS_3              10                50
  CLUS_4              24               130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       14     19     31
  8P GAIN WILD-TYPE     65     89     82
D15V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              14                65
  CLUS_2              19                89
  CLUS_3              31                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       24     12     28
  8P GAIN WILD-TYPE    122     47     67
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              24               122
  CLUS_2              12                47
  CLUS_3              28                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       30     40     22
  8P GAIN WILD-TYPE     91    142    122
D15V11, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              30                91
  CLUS_2              40               142
  CLUS_3              22               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 CLUS_4
  8P GAIN MUTATED       26     11     35     20
  8P GAIN WILD-TYPE     79     60    130     86
D15V12, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              26                79
  CLUS_2              11                60
  CLUS_3              35               130
  CLUS_4              20                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"
D15V13, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    3  0
  8P GAIN WILD-TYPE  9 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    0
  8P GAIN WILD-TYPE    9   10
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P GAIN MUTATED        0      0      1      0      1      1
  8P GAIN WILD-TYPE      6      2      1      6      3      1
D15V14, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               0                 2
  CLUS_3               1                 1
  CLUS_4               0                 6
  CLUS_5               1                 3
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       83     86     67
  8Q GAIN WILD-TYPE    132    130     59
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              83               132
  CLUS_2              86               130
  CLUS_3              67                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      115     87     34
  8Q GAIN WILD-TYPE    195     71     55
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1             115               195
  CLUS_2              87                71
  CLUS_3              34                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       77     71     86
  8Q GAIN WILD-TYPE     82     93    146
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              77                82
  CLUS_2              71                93
  CLUS_3              86               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8Q GAIN MUTATED       35      25     20     27     20     36     16     13
  8Q GAIN WILD-TYPE     50      32     38     55     14     39     18     23
                   vv
clus                CLUS_8 CLUS_9
  8Q GAIN MUTATED       19     23
  8Q GAIN WILD-TYPE     33     19
D16V4, multiclass
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               35                50
  CLUS_10              25                32
  CLUS_2               20                38
  CLUS_3               27                55
  CLUS_4               20                14
  CLUS_5               36                39
  CLUS_6               16                18
  CLUS_7               13                23
  CLUS_8               19                33
  CLUS_9               23                19
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       65     95     82
  8Q GAIN WILD-TYPE    106    111    120
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              65               106
  CLUS_2              95               111
  CLUS_3              82               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
  8Q GAIN MUTATED       79     70     89
  8Q GAIN WILD-TYPE     93    105    132
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              79                93
  CLUS_2              70               105
  CLUS_3              89               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
  8Q GAIN MUTATED       59     77     34
  8Q GAIN WILD-TYPE     87    112     42
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              59                87
  CLUS_2              77               112
  CLUS_3              34                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       61     25     26     58
  8Q GAIN WILD-TYPE     82     29     34     96
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              61                82
  CLUS_2              25                29
  CLUS_3              26                34
  CLUS_4              58                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
  8Q GAIN MUTATED       39     36     61
  8Q GAIN WILD-TYPE     40     72     52
D16V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              39                40
  CLUS_2              36                72
  CLUS_3              61                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       64     19     53
  8Q GAIN WILD-TYPE     82     40     42
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              64                82
  CLUS_2              19                40
  CLUS_3              53                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       56     78     57
  8Q GAIN WILD-TYPE     65    104     87
D16V11, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              56                65
  CLUS_2              78               104
  CLUS_3              57                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 CLUS_4
  8Q GAIN MUTATED       46     27     72     46
  8Q GAIN WILD-TYPE     59     44     93     60
D16V12, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              46                59
  CLUS_2              27                44
  CLUS_3              72                93
  CLUS_4              46                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                   cls
clus                0 1
  8Q GAIN MUTATED   7 1
  8Q GAIN WILD-TYPE 5 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7    1
  8Q GAIN WILD-TYPE    5    9
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                 5
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q GAIN MUTATED        3      0      1      1      2      1
  8Q GAIN WILD-TYPE      3      2      1      5      2      1
D16V14, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               0                 2
  CLUS_3               1                 1
  CLUS_4               1                 5
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       29     44     17
  9P GAIN WILD-TYPE    186    172    109
D17V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              29               186
  CLUS_2              44               172
  CLUS_3              17               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       56     22     12
  9P GAIN WILD-TYPE    254    136     77
D17V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              56               254
  CLUS_2              22               136
  CLUS_3              12                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       29     20     41
  9P GAIN WILD-TYPE    130    144    191
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              29               130
  CLUS_2              20               144
  CLUS_3              41               191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9P GAIN MUTATED       12       8      6     18      7     13      5      6
  9P GAIN WILD-TYPE     73      49     52     64     27     62     29     30
                   vv
clus                CLUS_8 CLUS_9
  9P GAIN MUTATED        9      6
  9P GAIN WILD-TYPE     43     36
D17V4, multiclass
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               12                73
  CLUS_10               8                49
  CLUS_2                6                52
  CLUS_3               18                64
  CLUS_4                7                27
  CLUS_5               13                62
  CLUS_6                5                29
  CLUS_7                6                30
  CLUS_8                9                43
  CLUS_9                6                36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     29     46
  9P GAIN WILD-TYPE    154    177    156
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              17               154
  CLUS_2              29               177
  CLUS_3              46               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       33     16     42
  9P GAIN WILD-TYPE    139    159    179
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              33               139
  CLUS_2              16               159
  CLUS_3              42               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       22     35     10
  9P GAIN WILD-TYPE    124    154     66
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              22               124
  CLUS_2              35               154
  CLUS_3              10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED       21      7     13     26
  9P GAIN WILD-TYPE    122     47     47    128
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              21               122
  CLUS_2               7                47
  CLUS_3              13                47
  CLUS_4              26               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       17     20     19
  9P GAIN WILD-TYPE     62     88     94
D17V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              17                62
  CLUS_2              20                88
  CLUS_3              19                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       27     13     16
  9P GAIN WILD-TYPE    119     46     79
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              27               119
  CLUS_2              13                46
  CLUS_3              16                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       20     38     19
  9P GAIN WILD-TYPE    101    144    125
D17V11, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              20               101
  CLUS_2              38               144
  CLUS_3              19               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
  9P GAIN MUTATED       15     11     37     14
  9P GAIN WILD-TYPE     90     60    128     92
D17V12, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              15                90
  CLUS_2              11                60
  CLUS_3              37               128
  CLUS_4              14                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"
D17V13, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  3
  9P GAIN WILD-TYPE 10  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    3
  9P GAIN WILD-TYPE   10    7
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               3                 7
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P GAIN MUTATED        1      0      0      1      2      1
  9P GAIN WILD-TYPE      5      2      2      5      2      1
D17V14, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED       12     20     12
  9Q GAIN WILD-TYPE    203    196    114
D18V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              12               203
  CLUS_2              20               196
  CLUS_3              12               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
  9Q GAIN MUTATED       24     16      4
  9Q GAIN WILD-TYPE    286    142     85
D18V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              24               286
  CLUS_2              16               142
  CLUS_3               4                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       19     11     14
  9Q GAIN WILD-TYPE    140    153    218
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              19               140
  CLUS_2              11               153
  CLUS_3              14               218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9Q GAIN MUTATED        8       4      2      9      2      9      0      3
  9Q GAIN WILD-TYPE     77      53     56     73     32     66     34     33
                   vv
clus                CLUS_8 CLUS_9
  9Q GAIN MUTATED        4      3
  9Q GAIN WILD-TYPE     48     39
D18V4, multiclass
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1                8                77
  CLUS_10               4                53
  CLUS_2                2                56
  CLUS_3                9                73
  CLUS_4                2                32
  CLUS_5                9                66
  CLUS_6                0                34
  CLUS_7                3                33
  CLUS_8                4                48
  CLUS_9                3                39
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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        9     22     14
  9Q GAIN WILD-TYPE    162    184    188
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               9               162
  CLUS_2              22               184
  CLUS_3              14               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       10     12     23
  9Q GAIN WILD-TYPE    162    163    198
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              10               162
  CLUS_2              12               163
  CLUS_3              23               198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        9     19      5
  9Q GAIN WILD-TYPE    137    170     71
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               9               137
  CLUS_2              19               170
  CLUS_3               5                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       11      2      8     12
  9Q GAIN WILD-TYPE    132     52     52    142
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              11               132
  CLUS_2               2                52
  CLUS_3               8                52
  CLUS_4              12               142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        7      8     16
  9Q GAIN WILD-TYPE     72    100     97
D18V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7                72
  CLUS_2               8               100
  CLUS_3              16                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED       16      3     12
  9Q GAIN WILD-TYPE    130     56     83
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              16               130
  CLUS_2               3                56
  CLUS_3              12                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED       11     18      9
  9Q GAIN WILD-TYPE    110    164    135
D18V11, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              11               110
  CLUS_2              18               164
  CLUS_3               9               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
  9Q GAIN MUTATED       11      5     15      7
  9Q GAIN WILD-TYPE     94     66    150     99
D18V12, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              11                94
  CLUS_2               5                66
  CLUS_3              15               150
  CLUS_4               7                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"
D18V13, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    0  1
  9Q GAIN WILD-TYPE 12  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    1
  9Q GAIN WILD-TYPE   12    9
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q GAIN MUTATED        1      0      0      0      0      0
  9Q GAIN WILD-TYPE      5      2      2      6      4      2
D18V14, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                21 
       TCGA-04-1652        TCGA-09-2050        TCGA-09-2054        TCGA-13-0908 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-23-2077        TCGA-24-1928        TCGA-24-2036        TCGA-24-2288 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-24-2289        TCGA-24-2290        TCGA-24-2297        TCGA-25-2392 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-25-2399        TCGA-25-2400        TCGA-57-1994        TCGA-59-2363 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-61-1918        TCGA-61-2088        TCGA-61-2098        TCGA-61-2109 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-61-2111 
"9Q GAIN WILD-TYPE" 

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       81     53     48
  10P GAIN WILD-TYPE    134    163     78
D19V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               81                134
  CLUS_2               53                163
  CLUS_3               48                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       90     52     40
  10P GAIN WILD-TYPE    220    106     49
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               90                220
  CLUS_2               52                106
  CLUS_3               40                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     53     80
  10P GAIN WILD-TYPE    111    111    152
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               48                111
  CLUS_2               53                111
  CLUS_3               80                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10P GAIN MUTATED       24      15     19     24     14     26     15     10
  10P GAIN WILD-TYPE     61      42     39     58     20     49     19     26
                    vv
clus                 CLUS_8 CLUS_9
  10P GAIN MUTATED       23     11
  10P GAIN WILD-TYPE     29     31
D19V4, multiclass
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                24                 61
  CLUS_10               15                 42
  CLUS_2                19                 39
  CLUS_3                24                 58
  CLUS_4                14                 20
  CLUS_5                26                 49
  CLUS_6                15                 19
  CLUS_7                10                 26
  CLUS_8                23                 29
  CLUS_9                11                 31
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       41     45    102
  10P GAIN WILD-TYPE    130    161    100
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               41                130
  CLUS_2               45                161
  CLUS_3              102                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       77     44     63
  10P GAIN WILD-TYPE     95    131    158
D19V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               77                 95
  CLUS_2               44                131
  CLUS_3               63                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
  10P GAIN MUTATED       43     62     25
  10P GAIN WILD-TYPE    103    127     51
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               43                103
  CLUS_2               62                127
  CLUS_3               25                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED       48     16     20     46
  10P GAIN WILD-TYPE     95     38     40    108
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               48                 95
  CLUS_2               16                 38
  CLUS_3               20                 40
  CLUS_4               46                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
  10P GAIN MUTATED       14     45     40
  10P GAIN WILD-TYPE     65     63     73
D19V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               14                 65
  CLUS_2               45                 63
  CLUS_3               40                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       42     26     31
  10P GAIN WILD-TYPE    104     33     64
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               42                104
  CLUS_2               26                 33
  CLUS_3               31                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       41     63     42
  10P GAIN WILD-TYPE     80    119    102
D19V11, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               41                 80
  CLUS_2               63                119
  CLUS_3               42                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED       22     27     70     27
  10P GAIN WILD-TYPE     83     44     95     79
D19V12, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               22                 83
  CLUS_2               27                 44
  CLUS_3               70                 95
  CLUS_4               27                 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"
D19V13, binary
                    cls
clus                 0 1
  10P GAIN MUTATED   5 4
  10P GAIN WILD-TYPE 7 6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    4
  10P GAIN WILD-TYPE    7    6
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                4                  6
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P GAIN MUTATED        2      1      0      3      2      1
  10P GAIN WILD-TYPE      4      1      2      3      2      1
D19V14, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                1                  1
  CLUS_3                0                  2
  CLUS_4                3                  3
  CLUS_5                2                  2
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       55     28     24
  10Q GAIN WILD-TYPE    160    188    102
D20V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               55                160
  CLUS_2               28                188
  CLUS_3               24                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       52     27     28
  10Q GAIN WILD-TYPE    258    131     61
D20V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               52                258
  CLUS_2               27                131
  CLUS_3               28                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       25     38     44
  10Q GAIN WILD-TYPE    134    126    188
D20V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               25                134
  CLUS_2               38                126
  CLUS_3               44                188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10Q GAIN MUTATED       12      10     15     13      3     14     10      6
  10Q GAIN WILD-TYPE     73      47     43     69     31     61     24     30
                    vv
clus                 CLUS_8 CLUS_9
  10Q GAIN MUTATED       17      7
  10Q GAIN WILD-TYPE     35     35
D20V4, multiclass
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                12                 73
  CLUS_10               10                 47
  CLUS_2                15                 43
  CLUS_3                13                 69
  CLUS_4                 3                 31
  CLUS_5                14                 61
  CLUS_6                10                 24
  CLUS_7                 6                 30
  CLUS_8                17                 35
  CLUS_9                 7                 35
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       24     33     54
  10Q GAIN WILD-TYPE    147    173    148
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               24                147
  CLUS_2               33                173
  CLUS_3               54                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
  10Q GAIN MUTATED       42     31     35
  10Q GAIN WILD-TYPE    130    144    186
D20V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               42                130
  CLUS_2               31                144
  CLUS_3               35                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     37     15
  10Q GAIN WILD-TYPE    123    152     61
D20V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               23                123
  CLUS_2               37                152
  CLUS_3               15                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       21     10      9     35
  10Q GAIN WILD-TYPE    122     44     51    119
D20V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               21                122
  CLUS_2               10                 44
  CLUS_3                9                 51
  CLUS_4               35                119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        7     27     20
  10Q GAIN WILD-TYPE     72     81     93
D20V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                7                 72
  CLUS_2               27                 81
  CLUS_3               20                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       21     17     16
  10Q GAIN WILD-TYPE    125     42     79
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               21                125
  CLUS_2               17                 42
  CLUS_3               16                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       19     35     27
  10Q GAIN WILD-TYPE    102    147    117
D20V11, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               19                102
  CLUS_2               35                147
  CLUS_3               27                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 CLUS_4
  10Q GAIN MUTATED       13     16     34     18
  10Q GAIN WILD-TYPE     92     55    131     88
D20V12, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               13                 92
  CLUS_2               16                 55
  CLUS_3               34                131
  CLUS_4               18                 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"
D20V13, binary
                    cls
clus                 0 1
  10Q GAIN MUTATED   4 2
  10Q GAIN WILD-TYPE 8 8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    2
  10Q GAIN WILD-TYPE    8    8
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q GAIN MUTATED        1      0      0      3      1      1
  10Q GAIN WILD-TYPE      5      2      2      3      3      1
D20V14, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                3                  3
  CLUS_5                1                  3
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       27     33     16
  11P GAIN WILD-TYPE    188    183    110
D21V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               27                188
  CLUS_2               33                183
  CLUS_3               16                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
  11P GAIN MUTATED       51     17      8
  11P GAIN WILD-TYPE    259    141     81
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               51                259
  CLUS_2               17                141
  CLUS_3                8                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       24     19     33
  11P GAIN WILD-TYPE    135    145    199
D21V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               24                135
  CLUS_2               19                145
  CLUS_3               33                199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P GAIN MUTATED       14       4      8     14      3     11      5      7
  11P GAIN WILD-TYPE     71      53     50     68     31     64     29     29
                    vv
clus                 CLUS_8 CLUS_9
  11P GAIN MUTATED        8      2
  11P GAIN WILD-TYPE     44     40
D21V4, multiclass
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                14                 71
  CLUS_10                4                 53
  CLUS_2                 8                 50
  CLUS_3                14                 68
  CLUS_4                 3                 31
  CLUS_5                11                 64
  CLUS_6                 5                 29
  CLUS_7                 7                 29
  CLUS_8                 8                 44
  CLUS_9                 2                 40
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       16     28     33
  11P GAIN WILD-TYPE    155    178    169
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               16                155
  CLUS_2               28                178
  CLUS_3               33                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       26     13     37
  11P GAIN WILD-TYPE    146    162    184
D21V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               26                146
  CLUS_2               13                162
  CLUS_3               37                184
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        9     32     11
  11P GAIN WILD-TYPE    137    157     65
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                9                137
  CLUS_2               32                157
  CLUS_3               11                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED       14      6      6     26
  11P GAIN WILD-TYPE    129     48     54    128
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               14                129
  CLUS_2                6                 48
  CLUS_3                6                 54
  CLUS_4               26                128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       12     13     19
  11P GAIN WILD-TYPE     67     95     94
D21V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               12                 67
  CLUS_2               13                 95
  CLUS_3               19                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       25      5     14
  11P GAIN WILD-TYPE    121     54     81
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               25                121
  CLUS_2                5                 54
  CLUS_3               14                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       14     29     19
  11P GAIN WILD-TYPE    107    153    125
D21V11, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               14                107
  CLUS_2               29                153
  CLUS_3               19                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
  11P GAIN MUTATED       14      8     26     14
  11P GAIN WILD-TYPE     91     63    139     92
D21V12, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               14                 91
  CLUS_2                8                 63
  CLUS_3               26                139
  CLUS_4               14                 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"
D21V13, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE 11  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    1
  11P GAIN WILD-TYPE   11    9
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P GAIN MUTATED        1      0      0      0      1      0
  11P GAIN WILD-TYPE      5      2      2      6      3      2
D21V14, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 20 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-2036 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-24-2288         TCGA-24-2289         TCGA-24-2290 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-24-2297         TCGA-25-2392         TCGA-25-2399 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-25-2404         TCGA-57-1994         TCGA-59-2363 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-61-1918         TCGA-61-2088         TCGA-61-2098 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-61-2109         TCGA-61-2111 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       38     49     23
  11Q GAIN WILD-TYPE    177    167    103
D22V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               38                177
  CLUS_2               49                167
  CLUS_3               23                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
  11Q GAIN MUTATED       69     27     14
  11Q GAIN WILD-TYPE    241    131     75
D22V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               69                241
  CLUS_2               27                131
  CLUS_3               14                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       33     33     44
  11Q GAIN WILD-TYPE    126    131    188
D22V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               33                126
  CLUS_2               33                131
  CLUS_3               44                188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q GAIN MUTATED       15       5     19     17      6     13      7     10
  11Q GAIN WILD-TYPE     70      52     39     65     28     62     27     26
                    vv
clus                 CLUS_8 CLUS_9
  11Q GAIN MUTATED       10      8
  11Q GAIN WILD-TYPE     42     34
D22V4, multiclass
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                15                 70
  CLUS_10                5                 52
  CLUS_2                19                 39
  CLUS_3                17                 65
  CLUS_4                 6                 28
  CLUS_5                13                 62
  CLUS_6                 7                 27
  CLUS_7                10                 26
  CLUS_8                10                 42
  CLUS_9                 8                 34
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       20     48     47
  11Q GAIN WILD-TYPE    151    158    155
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               20                151
  CLUS_2               48                158
  CLUS_3               47                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
  11Q GAIN MUTATED       38     20     55
  11Q GAIN WILD-TYPE    134    155    166
D22V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               38                134
  CLUS_2               20                155
  CLUS_3               55                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
  11Q GAIN MUTATED       21     42     14
  11Q GAIN WILD-TYPE    125    147     62
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               21                125
  CLUS_2               42                147
  CLUS_3               14                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       22      7     14     34
  11Q GAIN WILD-TYPE    121     47     46    120
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               22                121
  CLUS_2                7                 47
  CLUS_3               14                 46
  CLUS_4               34                120
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       16     20     28
  11Q GAIN WILD-TYPE     63     88     85
D22V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               16                 63
  CLUS_2               20                 88
  CLUS_3               28                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       33      8     23
  11Q GAIN WILD-TYPE    113     51     72
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               33                113
  CLUS_2                8                 51
  CLUS_3               23                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       19     39     31
  11Q GAIN WILD-TYPE    102    143    113
D22V11, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               19                102
  CLUS_2               39                143
  CLUS_3               31                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
  11Q GAIN MUTATED       22     12     31     24
  11Q GAIN WILD-TYPE     83     59    134     82
D22V12, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               22                 83
  CLUS_2               12                 59
  CLUS_3               31                134
  CLUS_4               24                 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"
D22V13, binary
                    cls
clus                 0 1
  11Q GAIN MUTATED   4 1
  11Q GAIN WILD-TYPE 8 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    1
  11Q GAIN WILD-TYPE    8    9
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q GAIN MUTATED        4      0      0      0      1      0
  11Q GAIN WILD-TYPE      2      2      2      6      3      2
D22V14, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                  2
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                0                  6
  CLUS_5                1                  3
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED      118     75     49
  12P GAIN WILD-TYPE     97    141     77
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1              118                 97
  CLUS_2               75                141
  CLUS_3               49                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED      132     57     53
  12P GAIN WILD-TYPE    178    101     36
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1              132                178
  CLUS_2               57                101
  CLUS_3               53                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       66     75    100
  12P GAIN WILD-TYPE     93     89    132
D23V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               66                 93
  CLUS_2               75                 89
  CLUS_3              100                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12P GAIN MUTATED       33      20     28     36     15     30     19     11
  12P GAIN WILD-TYPE     52      37     30     46     19     45     15     25
                    vv
clus                 CLUS_8 CLUS_9
  12P GAIN MUTATED       37     12
  12P GAIN WILD-TYPE     15     30
D23V4, multiclass
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                33                 52
  CLUS_10               20                 37
  CLUS_2                28                 30
  CLUS_3                36                 46
  CLUS_4                15                 19
  CLUS_5                30                 45
  CLUS_6                19                 15
  CLUS_7                11                 25
  CLUS_8                37                 15
  CLUS_9                12                 30
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       54     68    133
  12P GAIN WILD-TYPE    117    138     69
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               54                117
  CLUS_2               68                138
  CLUS_3              133                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED      104     71     74
  12P GAIN WILD-TYPE     68    104    147
D23V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1              104                 68
  CLUS_2               71                104
  CLUS_3               74                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
  12P GAIN MUTATED       66     84     24
  12P GAIN WILD-TYPE     80    105     52
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               66                 80
  CLUS_2               84                105
  CLUS_3               24                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED       62     20     28     64
  12P GAIN WILD-TYPE     81     34     32     90
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               62                 81
  CLUS_2               20                 34
  CLUS_3               28                 32
  CLUS_4               64                 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
  12P GAIN MUTATED       22     61     45
  12P GAIN WILD-TYPE     57     47     68
D23V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               22                 57
  CLUS_2               61                 47
  CLUS_3               45                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       53     38     37
  12P GAIN WILD-TYPE     93     21     58
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               53                 93
  CLUS_2               38                 21
  CLUS_3               37                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       53     70     69
  12P GAIN WILD-TYPE     68    112     75
D23V11, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               53                 68
  CLUS_2               70                112
  CLUS_3               69                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED       27     38     81     46
  12P GAIN WILD-TYPE     78     33     84     60
D23V12, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               27                 78
  CLUS_2               38                 33
  CLUS_3               81                 84
  CLUS_4               46                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                    cls
clus                 0 1
  12P GAIN MUTATED   6 3
  12P GAIN WILD-TYPE 6 7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6    3
  12P GAIN WILD-TYPE    6    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                6                  6
  CLUS_2                3                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P GAIN MUTATED        2      0      0      2      3      2
  12P GAIN WILD-TYPE      4      2      2      4      1      0
D23V14, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                2                  4
  CLUS_5                3                  1
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       81     50     38
  12Q GAIN WILD-TYPE    134    166     88
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               81                134
  CLUS_2               50                166
  CLUS_3               38                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       95     39     35
  12Q GAIN WILD-TYPE    215    119     54
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               95                215
  CLUS_2               39                119
  CLUS_3               35                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       51     45     72
  12Q GAIN WILD-TYPE    108    119    160
D24V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               51                108
  CLUS_2               45                119
  CLUS_3               72                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12Q GAIN MUTATED       27      16     21     21     11     20     15      9
  12Q GAIN WILD-TYPE     58      41     37     61     23     55     19     27
                    vv
clus                 CLUS_8 CLUS_9
  12Q GAIN MUTATED       23      5
  12Q GAIN WILD-TYPE     29     37
D24V4, multiclass
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                27                 58
  CLUS_10               16                 41
  CLUS_2                21                 37
  CLUS_3                21                 61
  CLUS_4                11                 23
  CLUS_5                20                 55
  CLUS_6                15                 19
  CLUS_7                 9                 27
  CLUS_8                23                 29
  CLUS_9                 5                 37
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       40     38     99
  12Q GAIN WILD-TYPE    131    168    103
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               40                131
  CLUS_2               38                168
  CLUS_3               99                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
  12Q GAIN MUTATED       78     43     54
  12Q GAIN WILD-TYPE     94    132    167
D24V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               78                 94
  CLUS_2               43                132
  CLUS_3               54                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
  12Q GAIN MUTATED       39     65     16
  12Q GAIN WILD-TYPE    107    124     60
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               39                107
  CLUS_2               65                124
  CLUS_3               16                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       41     12     20     47
  12Q GAIN WILD-TYPE    102     42     40    107
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               41                102
  CLUS_2               12                 42
  CLUS_3               20                 40
  CLUS_4               47                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
  12Q GAIN MUTATED       21     45     29
  12Q GAIN WILD-TYPE     58     63     84
D24V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               21                 58
  CLUS_2               45                 63
  CLUS_3               29                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       45     27     23
  12Q GAIN WILD-TYPE    101     32     72
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               45                101
  CLUS_2               27                 32
  CLUS_3               23                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       38     45     51
  12Q GAIN WILD-TYPE     83    137     93
D24V11, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               38                 83
  CLUS_2               45                137
  CLUS_3               51                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED       19     28     53     34
  12Q GAIN WILD-TYPE     86     43    112     72
D24V12, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               19                 86
  CLUS_2               28                 43
  CLUS_3               53                112
  CLUS_4               34                 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"
D24V13, binary
                    cls
clus                 0 1
  12Q GAIN MUTATED   6 1
  12Q GAIN WILD-TYPE 6 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      6    1
  12Q GAIN WILD-TYPE    6    9
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                6                  6
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q GAIN MUTATED        2      0      0      1      2      2
  12Q GAIN WILD-TYPE      4      2      2      5      2      0
D24V14, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                1                  5
  CLUS_5                2                  2
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       26     12     19
  13Q GAIN WILD-TYPE    189    204    107
D25V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               26                189
  CLUS_2               12                204
  CLUS_3               19                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
  13Q GAIN MUTATED       19     20     18
  13Q GAIN WILD-TYPE    291    138     71
D25V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               19                291
  CLUS_2               20                138
  CLUS_3               18                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       13     19     24
  13Q GAIN WILD-TYPE    146    145    208
D25V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               13                146
  CLUS_2               19                145
  CLUS_3               24                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q GAIN MUTATED        6       8      5      6      2     10      9      1
  13Q GAIN WILD-TYPE     79      49     53     76     32     65     25     35
                    vv
clus                 CLUS_8 CLUS_9
  13Q GAIN MUTATED        8      1
  13Q GAIN WILD-TYPE     44     41
D25V4, multiclass
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                 6                 79
  CLUS_10                8                 49
  CLUS_2                 5                 53
  CLUS_3                 6                 76
  CLUS_4                 2                 32
  CLUS_5                10                 65
  CLUS_6                 9                 25
  CLUS_7                 1                 35
  CLUS_8                 8                 44
  CLUS_9                 1                 41
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       22      7     31
  13Q GAIN WILD-TYPE    149    199    171
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               22                149
  CLUS_2                7                199
  CLUS_3               31                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
  13Q GAIN MUTATED       31     20      8
  13Q GAIN WILD-TYPE    141    155    213
D25V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               31                141
  CLUS_2               20                155
  CLUS_3                8                213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       18     15      5
  13Q GAIN WILD-TYPE    128    174     71
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               18                128
  CLUS_2               15                174
  CLUS_3                5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       15      4      6     13
  13Q GAIN WILD-TYPE    128     50     54    141
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               15                128
  CLUS_2                4                 50
  CLUS_3                6                 54
  CLUS_4               13                141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        3     15     16
  13Q GAIN WILD-TYPE     76     93     97
D25V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 76
  CLUS_2               15                 93
  CLUS_3               16                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       11      9     14
  13Q GAIN WILD-TYPE    135     50     81
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               11                135
  CLUS_2                9                 50
  CLUS_3               14                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       18     14     15
  13Q GAIN WILD-TYPE    103    168    129
D25V11, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               18                103
  CLUS_2               14                168
  CLUS_3               15                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
  13Q GAIN MUTATED        6      5     24     12
  13Q GAIN WILD-TYPE     99     66    141     94
D25V12, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                 99
  CLUS_2                5                 66
  CLUS_3               24                141
  CLUS_4               12                 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"
D25V13, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    0  1
  13Q GAIN WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    1
  13Q GAIN WILD-TYPE   12    9
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q GAIN MUTATED        0      0      0      1      0      0
  13Q GAIN WILD-TYPE      6      2      2      5      4      2
D25V14, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 21 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2392 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-25-2399         TCGA-25-2400         TCGA-25-2404 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-57-1994         TCGA-59-2363         TCGA-61-1918 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-61-2088         TCGA-61-2109         TCGA-61-2111 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       28     16     14
  14Q GAIN WILD-TYPE    187    200    112
D26V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               28                187
  CLUS_2               16                200
  CLUS_3               14                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
  14Q GAIN MUTATED       26     21     11
  14Q GAIN WILD-TYPE    284    137     78
D26V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               26                284
  CLUS_2               21                137
  CLUS_3               11                 78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       13     21     24
  14Q GAIN WILD-TYPE    146    143    208
D26V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               13                146
  CLUS_2               21                143
  CLUS_3               24                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  14Q GAIN MUTATED        7       8      7      9      4      5      3      6
  14Q GAIN WILD-TYPE     78      49     51     73     30     70     31     30
                    vv
clus                 CLUS_8 CLUS_9
  14Q GAIN MUTATED        7      2
  14Q GAIN WILD-TYPE     45     40
D26V4, multiclass
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                 7                 78
  CLUS_10                8                 49
  CLUS_2                 7                 51
  CLUS_3                 9                 73
  CLUS_4                 4                 30
  CLUS_5                 5                 70
  CLUS_6                 3                 31
  CLUS_7                 6                 30
  CLUS_8                 7                 45
  CLUS_9                 2                 40
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     23     16
  14Q GAIN WILD-TYPE    151    183    186
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               20                151
  CLUS_2               23                183
  CLUS_3               16                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     16     22
  14Q GAIN WILD-TYPE    152    159    199
D26V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               20                152
  CLUS_2               16                159
  CLUS_3               22                199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       12     21      6
  14Q GAIN WILD-TYPE    134    168     70
D26V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               12                134
  CLUS_2               21                168
  CLUS_3                6                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED       12      7      4     16
  14Q GAIN WILD-TYPE    131     47     56    138
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               12                131
  CLUS_2                7                 47
  CLUS_3                4                 56
  CLUS_4               16                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        7     13     12
  14Q GAIN WILD-TYPE     72     95    101
D26V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                7                 72
  CLUS_2               13                 95
  CLUS_3               12                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       14      7     11
  14Q GAIN WILD-TYPE    132     52     84
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               14                132
  CLUS_2                7                 52
  CLUS_3               11                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       13     16     17
  14Q GAIN WILD-TYPE    108    166    127
D26V11, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               13                108
  CLUS_2               16                166
  CLUS_3               17                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 CLUS_4
  14Q GAIN MUTATED       10      5     17     14
  14Q GAIN WILD-TYPE     95     66    148     92
D26V12, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               10                 95
  CLUS_2                5                 66
  CLUS_3               17                148
  CLUS_4               14                 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"
D26V13, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    1  0
  14Q GAIN WILD-TYPE 11 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    0
  14Q GAIN WILD-TYPE   11   10
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q GAIN MUTATED        1      0      0      0      0      0
  14Q GAIN WILD-TYPE      5      2      2      6      4      2
D26V14, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 21 
        TCGA-09-2050         TCGA-09-2054         TCGA-13-0908 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-23-2077         TCGA-24-1928         TCGA-24-2036 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-24-2288         TCGA-24-2289         TCGA-24-2290 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-24-2297         TCGA-25-2392         TCGA-25-2399 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-25-2400         TCGA-25-2404         TCGA-57-1994 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-59-2363         TCGA-61-1918         TCGA-61-2088 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-61-2098         TCGA-61-2109         TCGA-61-2111 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED       15     16      7
  15Q GAIN WILD-TYPE    200    200    119
D27V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               15                200
  CLUS_2               16                200
  CLUS_3                7                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
  15Q GAIN MUTATED       25      8      5
  15Q GAIN WILD-TYPE    285    150     84
D27V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               25                285
  CLUS_2                8                150
  CLUS_3                5                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED       17      9     12
  15Q GAIN WILD-TYPE    142    155    220
D27V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               17                142
  CLUS_2                9                155
  CLUS_3               12                220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  15Q GAIN MUTATED        9       5      3      4      0      5      2      3
  15Q GAIN WILD-TYPE     76      52     55     78     34     70     32     33
                    vv
clus                 CLUS_8 CLUS_9
  15Q GAIN MUTATED        4      3
  15Q GAIN WILD-TYPE     48     39
D27V4, multiclass
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                 9                 76
  CLUS_10                5                 52
  CLUS_2                 3                 55
  CLUS_3                 4                 78
  CLUS_4                 0                 34
  CLUS_5                 5                 70
  CLUS_6                 2                 32
  CLUS_7                 3                 33
  CLUS_8                 4                 48
  CLUS_9                 3                 39
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       13     19      8
  15Q GAIN WILD-TYPE    158    187    194
D27V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1               13                158
  CLUS_2               19                187
  CLUS_3                8                194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        9     14     16
  15Q GAIN WILD-TYPE    163    161    205
D27V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                9                163
  CLUS_2               14                161
  CLUS_3               16                205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        8     11      2
  15Q GAIN WILD-TYPE    138    178     74
D27V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                8                138
  CLUS_2               11                178
  CLUS_3                2                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        5      0      3     13
  15Q GAIN WILD-TYPE    138     54     57    141
D27V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                138
  CLUS_2                0                 54
  CLUS_3                3                 57
  CLUS_4               13                141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        5      7      4
  15Q GAIN WILD-TYPE     74    101    109
D27V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                 74
  CLUS_2                7                101
  CLUS_3                4                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        7      5      4
  15Q GAIN WILD-TYPE    139     54     91
D27V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                7                139
  CLUS_2                5                 54
  CLUS_3                4                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        5      9     12
  15Q GAIN WILD-TYPE    116    173    132
D27V11, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                116
  CLUS_2                9                173
  CLUS_3               12                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
  15Q GAIN MUTATED        5      3      7     11
  15Q GAIN WILD-TYPE    100     68    158     95
D27V12, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                100
  CLUS_2                3                 68
  CLUS_3                7                158
  CLUS_4               11                 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"
D27V13, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    1  0
  15Q GAIN WILD-TYPE 11 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    0
  15Q GAIN WILD-TYPE   11   10
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q GAIN MUTATED        0      0      0      1      0      0
  15Q GAIN WILD-TYPE      6      2      2      5      4      2
D27V14, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 21 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2392 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-25-2399         TCGA-25-2400         TCGA-25-2404 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-59-2363         TCGA-61-1918         TCGA-61-2088 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-61-2098         TCGA-61-2109         TCGA-61-2111 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       34     18      6
  16P GAIN WILD-TYPE    181    198    120
D28V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               34                181
  CLUS_2               18                198
  CLUS_3                6                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
  16P GAIN MUTATED       34      8     16
  16P GAIN WILD-TYPE    276    150     73
D28V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               34                276
  CLUS_2                8                150
  CLUS_3               16                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       13     21     24
  16P GAIN WILD-TYPE    146    143    208
D28V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               13                146
  CLUS_2               21                143
  CLUS_3               24                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16P GAIN MUTATED        7       7     10     11      1      5      4      1
  16P GAIN WILD-TYPE     78      50     48     71     33     70     30     35
                    vv
clus                 CLUS_8 CLUS_9
  16P GAIN MUTATED        9      3
  16P GAIN WILD-TYPE     43     39
D28V4, multiclass
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                 7                 78
  CLUS_10                7                 50
  CLUS_2                10                 48
  CLUS_3                11                 71
  CLUS_4                 1                 33
  CLUS_5                 5                 70
  CLUS_6                 4                 30
  CLUS_7                 1                 35
  CLUS_8                 9                 43
  CLUS_9                 3                 39
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     15     30
  16P GAIN WILD-TYPE    157    191    172
D28V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               14                157
  CLUS_2               15                191
  CLUS_3               30                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       23      9     26
  16P GAIN WILD-TYPE    149    166    195
D28V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               23                149
  CLUS_2                9                166
  CLUS_3               26                195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       13     23      8
  16P GAIN WILD-TYPE    133    166     68
D28V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               13                133
  CLUS_2               23                166
  CLUS_3                8                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED       11      3      9     21
  16P GAIN WILD-TYPE    132     51     51    133
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               11                132
  CLUS_2                3                 51
  CLUS_3                9                 51
  CLUS_4               21                133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        5     14      7
  16P GAIN WILD-TYPE     74     94    106
D28V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 74
  CLUS_2               14                 94
  CLUS_3                7                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       14      5      7
  16P GAIN WILD-TYPE    132     54     88
D28V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               14                132
  CLUS_2                5                 54
  CLUS_3                7                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        8     16     20
  16P GAIN WILD-TYPE    113    166    124
D28V11, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                8                113
  CLUS_2               16                166
  CLUS_3               20                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
  16P GAIN MUTATED        4      9     18     13
  16P GAIN WILD-TYPE    101     62    147     93
D28V12, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                101
  CLUS_2                9                 62
  CLUS_3               18                147
  CLUS_4               13                 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"
D28V13, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  0
  16P GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    0
  16P GAIN WILD-TYPE   10   10
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P GAIN MUTATED        1      0      0      0      1      0
  16P GAIN WILD-TYPE      5      2      2      6      3      2
D28V14, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 20 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2392 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-25-2399         TCGA-25-2400         TCGA-25-2404 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-57-1994         TCGA-59-2363         TCGA-61-2088 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-61-2098         TCGA-61-2109 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       18     12      0
  16Q GAIN WILD-TYPE    197    204    126
D29V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               18                197
  CLUS_2               12                204
  CLUS_3                0                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
  16Q GAIN MUTATED       20      3      7
  16Q GAIN WILD-TYPE    290    155     82
D29V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               20                290
  CLUS_2                3                155
  CLUS_3                7                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        5     13     12
  16Q GAIN WILD-TYPE    154    151    220
D29V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                154
  CLUS_2               13                151
  CLUS_3               12                220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q GAIN MUTATED        4       5      8      3      0      2      2      1
  16Q GAIN WILD-TYPE     81      52     50     79     34     73     32     35
                    vv
clus                 CLUS_8 CLUS_9
  16Q GAIN MUTATED        3      2
  16Q GAIN WILD-TYPE     49     40
D29V4, multiclass
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                 4                 81
  CLUS_10                5                 52
  CLUS_2                 8                 50
  CLUS_3                 3                 79
  CLUS_4                 0                 34
  CLUS_5                 2                 73
  CLUS_6                 2                 32
  CLUS_7                 1                 35
  CLUS_8                 3                 49
  CLUS_9                 2                 40
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      8     15
  16Q GAIN WILD-TYPE    163    198    187
D29V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                163
  CLUS_2                8                198
  CLUS_3               15                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED       10      2     18
  16Q GAIN WILD-TYPE    162    173    203
D29V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                162
  CLUS_2                2                173
  CLUS_3               18                203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     13      4
  16Q GAIN WILD-TYPE    138    176     72
D29V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                138
  CLUS_2               13                176
  CLUS_3                4                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        6      2      2     15
  16Q GAIN WILD-TYPE    137     52     58    139
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                137
  CLUS_2                2                 52
  CLUS_3                2                 58
  CLUS_4               15                139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        3      9      2
  16Q GAIN WILD-TYPE     76     99    111
D29V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 76
  CLUS_2                9                 99
  CLUS_3                2                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
  16Q GAIN MUTATED        8      4      2
  16Q GAIN WILD-TYPE    138     55     93
D29V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                138
  CLUS_2                4                 55
  CLUS_3                2                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        0      9     13
  16Q GAIN WILD-TYPE    121    173    131
D29V11, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                121
  CLUS_2                9                173
  CLUS_3               13                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
  16Q GAIN MUTATED        2      6      6      8
  16Q GAIN WILD-TYPE    103     65    159     98
D29V12, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                103
  CLUS_2                6                 65
  CLUS_3                6                159
  CLUS_4                8                 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"
D29V13, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    1  0
  16Q GAIN WILD-TYPE 11 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    0
  16Q GAIN WILD-TYPE   11   10
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q GAIN MUTATED        1      0      0      0      0      0
  16Q GAIN WILD-TYPE      5      2      2      6      4      2
D29V14, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 21 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2392 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-25-2399         TCGA-25-2400         TCGA-25-2404 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-57-1994         TCGA-59-2363         TCGA-61-2088 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-61-2098         TCGA-61-2109         TCGA-61-2111 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       11      7      3
  17P GAIN WILD-TYPE    204    209    123
D30V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               11                204
  CLUS_2                7                209
  CLUS_3                3                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
  17P GAIN MUTATED       10      4      7
  17P GAIN WILD-TYPE    300    154     82
D30V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               10                300
  CLUS_2                4                154
  CLUS_3                7                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        2     10      9
  17P GAIN WILD-TYPE    157    154    223
D30V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                157
  CLUS_2               10                154
  CLUS_3                9                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P GAIN MUTATED        1       1      2      2      0      2      1      2
  17P GAIN WILD-TYPE     84      56     56     80     34     73     33     34
                    vv
clus                 CLUS_8 CLUS_9
  17P GAIN MUTATED        7      3
  17P GAIN WILD-TYPE     45     39
D30V4, multiclass
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                 1                 84
  CLUS_10                1                 56
  CLUS_2                 2                 56
  CLUS_3                 2                 80
  CLUS_4                 0                 34
  CLUS_5                 2                 73
  CLUS_6                 1                 33
  CLUS_7                 2                 34
  CLUS_8                 7                 45
  CLUS_9                 3                 39
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        4      6     12
  17P GAIN WILD-TYPE    167    200    190
D30V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                167
  CLUS_2                6                200
  CLUS_3               12                190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       10      4      8
  17P GAIN WILD-TYPE    162    171    213
D30V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               10                162
  CLUS_2                4                171
  CLUS_3                8                213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        6      9      1
  17P GAIN WILD-TYPE    140    180     75
D30V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                140
  CLUS_2                9                180
  CLUS_3                1                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        5      2      4      5
  17P GAIN WILD-TYPE    138     52     56    149
D30V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                138
  CLUS_2                2                 52
  CLUS_3                4                 56
  CLUS_4                5                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        2      7      5
  17P GAIN WILD-TYPE     77    101    108
D30V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                7                101
  CLUS_3                5                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
  17P GAIN MUTATED        5      6      3
  17P GAIN WILD-TYPE    141     53     92
D30V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                141
  CLUS_2                6                 53
  CLUS_3                3                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        1      8      6
  17P GAIN WILD-TYPE    120    174    138
D30V11, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                8                174
  CLUS_3                6                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        2      3      6      4
  17P GAIN WILD-TYPE    103     68    159    102
D30V12, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                103
  CLUS_2                3                 68
  CLUS_3                6                159
  CLUS_4                4                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  0
  17P GAIN WILD-TYPE 12 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    0
  17P GAIN WILD-TYPE   12   10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P GAIN MUTATED        0      0      0      0      0      0
  17P GAIN WILD-TYPE      6      2      2      6      4      2
D30V14, multiclass

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       16     16     14
  17Q GAIN WILD-TYPE    199    200    112
D31V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               16                199
  CLUS_2               16                200
  CLUS_3               14                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
  17Q GAIN MUTATED       18     16     12
  17Q GAIN WILD-TYPE    292    142     77
D31V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               18                292
  CLUS_2               16                142
  CLUS_3               12                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       11     15     20
  17Q GAIN WILD-TYPE    148    149    212
D31V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               11                148
  CLUS_2               15                149
  CLUS_3               20                212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q GAIN MUTATED        8       5      5      4      1      3      0      4
  17Q GAIN WILD-TYPE     77      52     53     78     33     72     34     32
                    vv
clus                 CLUS_8 CLUS_9
  17Q GAIN MUTATED       10      6
  17Q GAIN WILD-TYPE     42     36
D31V4, multiclass
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                 8                 77
  CLUS_10                5                 52
  CLUS_2                 5                 53
  CLUS_3                 4                 78
  CLUS_4                 1                 33
  CLUS_5                 3                 72
  CLUS_6                 0                 34
  CLUS_7                 4                 32
  CLUS_8                10                 42
  CLUS_9                 6                 36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       12     15     20
  17Q GAIN WILD-TYPE    159    191    182
D31V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               12                159
  CLUS_2               15                191
  CLUS_3               20                182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       18     11     18
  17Q GAIN WILD-TYPE    154    164    203
D31V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               18                154
  CLUS_2               11                164
  CLUS_3               18                203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       12     18      5
  17Q GAIN WILD-TYPE    134    171     71
D31V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               12                134
  CLUS_2               18                171
  CLUS_3                5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       14      4      6     11
  17Q GAIN WILD-TYPE    129     50     54    143
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               14                129
  CLUS_2                4                 50
  CLUS_3                6                 54
  CLUS_4               11                143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        8     10     11
  17Q GAIN WILD-TYPE     71     98    102
D31V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                 71
  CLUS_2               10                 98
  CLUS_3               11                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       12      9      8
  17Q GAIN WILD-TYPE    134     50     87
D31V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               12                134
  CLUS_2                9                 50
  CLUS_3                8                 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
  17Q GAIN MUTATED       10     14     14
  17Q GAIN WILD-TYPE    111    168    130
D31V11, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               10                111
  CLUS_2               14                168
  CLUS_3               14                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
  17Q GAIN MUTATED        9      5     13     11
  17Q GAIN WILD-TYPE     96     66    152     95
D31V12, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                 96
  CLUS_2                5                 66
  CLUS_3               13                152
  CLUS_4               11                 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"
D31V13, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  1
  17Q GAIN WILD-TYPE 11  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    1
  17Q GAIN WILD-TYPE   11    9
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q GAIN MUTATED        0      0      0      1      0      1
  17Q GAIN WILD-TYPE      6      2      2      5      4      1
D31V14, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2399 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-25-2400         TCGA-25-2404         TCGA-57-1994 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-59-2363         TCGA-61-1918         TCGA-61-2088 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-61-2109         TCGA-61-2111 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       53     42     21
  18P GAIN WILD-TYPE    162    174    105
D32V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               53                162
  CLUS_2               42                174
  CLUS_3               21                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       67     25     24
  18P GAIN WILD-TYPE    243    133     65
D32V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               67                243
  CLUS_2               25                133
  CLUS_3               24                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       33     36     46
  18P GAIN WILD-TYPE    126    128    186
D32V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               33                126
  CLUS_2               36                128
  CLUS_3               46                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P GAIN MUTATED       13      16     12     19      6     11     10     10
  18P GAIN WILD-TYPE     72      41     46     63     28     64     24     26
                    vv
clus                 CLUS_8 CLUS_9
  18P GAIN MUTATED       12      6
  18P GAIN WILD-TYPE     40     36
D32V4, multiclass
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                13                 72
  CLUS_10               16                 41
  CLUS_2                12                 46
  CLUS_3                19                 63
  CLUS_4                 6                 28
  CLUS_5                11                 64
  CLUS_6                10                 24
  CLUS_7                10                 26
  CLUS_8                12                 40
  CLUS_9                 6                 36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       26     35     59
  18P GAIN WILD-TYPE    145    171    143
D32V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               26                145
  CLUS_2               35                171
  CLUS_3               59                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
  18P GAIN MUTATED       54     26     38
  18P GAIN WILD-TYPE    118    149    183
D32V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               54                118
  CLUS_2               26                149
  CLUS_3               38                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       26     45      9
  18P GAIN WILD-TYPE    120    144     67
D32V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               26                120
  CLUS_2               45                144
  CLUS_3                9                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED       26     10     13     31
  18P GAIN WILD-TYPE    117     44     47    123
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               26                117
  CLUS_2               10                 44
  CLUS_3               13                 47
  CLUS_4               31                123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        9     26     21
  18P GAIN WILD-TYPE     70     82     92
D32V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                 70
  CLUS_2               26                 82
  CLUS_3               21                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       28     12     16
  18P GAIN WILD-TYPE    118     47     79
D32V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               28                118
  CLUS_2               12                 47
  CLUS_3               16                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       23     43     25
  18P GAIN WILD-TYPE     98    139    119
D32V11, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               23                 98
  CLUS_2               43                139
  CLUS_3               25                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
  18P GAIN MUTATED       15     17     39     20
  18P GAIN WILD-TYPE     90     54    126     86
D32V12, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               15                 90
  CLUS_2               17                 54
  CLUS_3               39                126
  CLUS_4               20                 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"
D32V13, binary
                    cls
clus                 0 1
  18P GAIN MUTATED   4 2
  18P GAIN WILD-TYPE 8 8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    2
  18P GAIN WILD-TYPE    8    8
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P GAIN MUTATED        2      0      0      2      2      0
  18P GAIN WILD-TYPE      4      2      2      4      2      2
D32V14, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                2                  4
  CLUS_5                2                  2
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       28     30     13
  18Q GAIN WILD-TYPE    187    186    113
D33V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               28                187
  CLUS_2               30                186
  CLUS_3               13                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
  18Q GAIN MUTATED       40     15     16
  18Q GAIN WILD-TYPE    270    143     73
D33V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               40                270
  CLUS_2               15                143
  CLUS_3               16                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       15     26     29
  18Q GAIN WILD-TYPE    144    138    203
D33V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               15                144
  CLUS_2               26                138
  CLUS_3               29                203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18Q GAIN MUTATED        5      10      7     12      5      8      5      8
  18Q GAIN WILD-TYPE     80      47     51     70     29     67     29     28
                    vv
clus                 CLUS_8 CLUS_9
  18Q GAIN MUTATED        6      4
  18Q GAIN WILD-TYPE     46     38
D33V4, multiclass
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                 5                 80
  CLUS_10               10                 47
  CLUS_2                 7                 51
  CLUS_3                12                 70
  CLUS_4                 5                 29
  CLUS_5                 8                 67
  CLUS_6                 5                 29
  CLUS_7                 8                 28
  CLUS_8                 6                 46
  CLUS_9                 4                 38
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       14     23     35
  18Q GAIN WILD-TYPE    157    183    167
D33V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               14                157
  CLUS_2               23                183
  CLUS_3               35                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
  18Q GAIN MUTATED       32     17     23
  18Q GAIN WILD-TYPE    140    158    198
D33V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               32                140
  CLUS_2               17                158
  CLUS_3               23                198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       17     22      8
  18Q GAIN WILD-TYPE    129    167     68
D33V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               17                129
  CLUS_2               22                167
  CLUS_3                8                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED       17      5      8     17
  18Q GAIN WILD-TYPE    126     49     52    137
D33V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               17                126
  CLUS_2                5                 49
  CLUS_3                8                 52
  CLUS_4               17                137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        7     14     15
  18Q GAIN WILD-TYPE     72     94     98
D33V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                7                 72
  CLUS_2               14                 94
  CLUS_3               15                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       20      5     11
  18Q GAIN WILD-TYPE    126     54     84
D33V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               20                126
  CLUS_2                5                 54
  CLUS_3               11                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       13     30     13
  18Q GAIN WILD-TYPE    108    152    131
D33V11, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               13                108
  CLUS_2               30                152
  CLUS_3               13                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
  18Q GAIN MUTATED        9     10     27     10
  18Q GAIN WILD-TYPE     96     61    138     96
D33V12, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                9                 96
  CLUS_2               10                 61
  CLUS_3               27                138
  CLUS_4               10                 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"
D33V13, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    2  1
  18Q GAIN WILD-TYPE 10  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    1
  18Q GAIN WILD-TYPE   10    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q GAIN MUTATED        1      0      0      1      1      0
  18Q GAIN WILD-TYPE      5      2      2      5      3      2
D33V14, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                1                  5
  CLUS_5                1                  3
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       75     60     30
  19P GAIN WILD-TYPE    140    156     96
D34V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               75                140
  CLUS_2               60                156
  CLUS_3               30                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       98     41     26
  19P GAIN WILD-TYPE    212    117     63
D34V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               98                212
  CLUS_2               41                117
  CLUS_3               26                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       48     43     73
  19P GAIN WILD-TYPE    111    121    159
D34V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               48                111
  CLUS_2               43                121
  CLUS_3               73                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P GAIN MUTATED       22      18     16     23     10     23      6     11
  19P GAIN WILD-TYPE     63      39     42     59     24     52     28     25
                    vv
clus                 CLUS_8 CLUS_9
  19P GAIN MUTATED       26      9
  19P GAIN WILD-TYPE     26     33
D34V4, multiclass
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                22                 63
  CLUS_10               18                 39
  CLUS_2                16                 42
  CLUS_3                23                 59
  CLUS_4                10                 24
  CLUS_5                23                 52
  CLUS_6                 6                 28
  CLUS_7                11                 25
  CLUS_8                26                 26
  CLUS_9                 9                 33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       33     55     83
  19P GAIN WILD-TYPE    138    151    119
D34V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               33                138
  CLUS_2               55                151
  CLUS_3               83                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
  19P GAIN MUTATED       60     39     69
  19P GAIN WILD-TYPE    112    136    152
D34V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               60                112
  CLUS_2               39                136
  CLUS_3               69                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
  19P GAIN MUTATED       41     63     18
  19P GAIN WILD-TYPE    105    126     58
D34V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               41                105
  CLUS_2               63                126
  CLUS_3               18                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED       40     16     16     50
  19P GAIN WILD-TYPE    103     38     44    104
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               40                103
  CLUS_2               16                 38
  CLUS_3               16                 44
  CLUS_4               50                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       16     32     34
  19P GAIN WILD-TYPE     63     76     79
D34V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               16                 63
  CLUS_2               32                 76
  CLUS_3               34                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       33     20     29
  19P GAIN WILD-TYPE    113     39     66
D34V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               33                113
  CLUS_2               20                 39
  CLUS_3               29                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       33     60     36
  19P GAIN WILD-TYPE     88    122    108
D34V11, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               33                 88
  CLUS_2               60                122
  CLUS_3               36                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 CLUS_4
  19P GAIN MUTATED       33     14     50     32
  19P GAIN WILD-TYPE     72     57    115     74
D34V12, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               33                 72
  CLUS_2               14                 57
  CLUS_3               50                115
  CLUS_4               32                 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"
D34V13, binary
                    cls
clus                 0 1
  19P GAIN MUTATED   3 3
  19P GAIN WILD-TYPE 9 7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    3
  19P GAIN WILD-TYPE    9    7
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                3                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P GAIN MUTATED        2      1      0      1      2      0
  19P GAIN WILD-TYPE      4      1      2      5      2      2
D34V14, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                1                  1
  CLUS_3                0                  2
  CLUS_4                1                  5
  CLUS_5                2                  2
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       69     54     34
  19Q GAIN WILD-TYPE    146    162     92
D35V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               69                146
  CLUS_2               54                162
  CLUS_3               34                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       86     43     28
  19Q GAIN WILD-TYPE    224    115     61
D35V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               86                224
  CLUS_2               43                115
  CLUS_3               28                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       44     44     67
  19Q GAIN WILD-TYPE    115    120    165
D35V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               44                115
  CLUS_2               44                120
  CLUS_3               67                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19Q GAIN MUTATED       21      16     17     18      9     21      8     11
  19Q GAIN WILD-TYPE     64      41     41     64     25     54     26     25
                    vv
clus                 CLUS_8 CLUS_9
  19Q GAIN MUTATED       25      9
  19Q GAIN WILD-TYPE     27     33
D35V4, multiclass
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                21                 64
  CLUS_10               16                 41
  CLUS_2                17                 41
  CLUS_3                18                 64
  CLUS_4                 9                 25
  CLUS_5                21                 54
  CLUS_6                 8                 26
  CLUS_7                11                 25
  CLUS_8                25                 27
  CLUS_9                 9                 33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     49     79
  19Q GAIN WILD-TYPE    138    157    123
D35V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               33                138
  CLUS_2               49                157
  CLUS_3               79                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
  19Q GAIN MUTATED       58     43     58
  19Q GAIN WILD-TYPE    114    132    163
D35V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               58                114
  CLUS_2               43                132
  CLUS_3               58                163
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       42     58     18
  19Q GAIN WILD-TYPE    104    131     58
D35V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               42                104
  CLUS_2               58                131
  CLUS_3               18                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED       33     17     20     48
  19Q GAIN WILD-TYPE    110     37     40    106
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               33                110
  CLUS_2               17                 37
  CLUS_3               20                 40
  CLUS_4               48                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
  19Q GAIN MUTATED       16     28     34
  19Q GAIN WILD-TYPE     63     80     79
D35V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               16                 63
  CLUS_2               28                 80
  CLUS_3               34                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       32     19     27
  19Q GAIN WILD-TYPE    114     40     68
D35V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               32                114
  CLUS_2               19                 40
  CLUS_3               27                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       31     58     35
  19Q GAIN WILD-TYPE     90    124    109
D35V11, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               31                 90
  CLUS_2               58                124
  CLUS_3               35                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED       28     16     50     30
  19Q GAIN WILD-TYPE     77     55    115     76
D35V12, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               28                 77
  CLUS_2               16                 55
  CLUS_3               50                115
  CLUS_4               30                 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"
D35V13, binary
                    cls
clus                 0 1
  19Q GAIN MUTATED   3 1
  19Q GAIN WILD-TYPE 9 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    1
  19Q GAIN WILD-TYPE    9    9
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q GAIN MUTATED        2      0      0      1      0      1
  19Q GAIN WILD-TYPE      4      2      2      5      4      1
D35V14, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                1                  5
  CLUS_5                0                  4
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED      125     88     64
  20P GAIN WILD-TYPE     90    128     62
D36V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1              125                 90
  CLUS_2               88                128
  CLUS_3               64                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      147     70     60
  20P GAIN WILD-TYPE    163     88     29
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1              147                163
  CLUS_2               70                 88
  CLUS_3               60                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       75     82    119
  20P GAIN WILD-TYPE     84     82    113
D36V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               75                 84
  CLUS_2               82                 82
  CLUS_3              119                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P GAIN MUTATED       31      27     33     36     21     41     26     16
  20P GAIN WILD-TYPE     54      30     25     46     13     34      8     20
                    vv
clus                 CLUS_8 CLUS_9
  20P GAIN MUTATED       32     13
  20P GAIN WILD-TYPE     20     29
D36V4, multiclass
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                31                 54
  CLUS_10               27                 30
  CLUS_2                33                 25
  CLUS_3                36                 46
  CLUS_4                21                 13
  CLUS_5                41                 34
  CLUS_6                26                  8
  CLUS_7                16                 20
  CLUS_8                32                 20
  CLUS_9                13                 29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       66     79    144
  20P GAIN WILD-TYPE    105    127     58
D36V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               66                105
  CLUS_2               79                127
  CLUS_3              144                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED      117     79     86
  20P GAIN WILD-TYPE     55     96    135
D36V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1              117                 55
  CLUS_2               79                 96
  CLUS_3               86                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
  20P GAIN MUTATED       74    103     34
  20P GAIN WILD-TYPE     72     86     42
D36V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               74                 72
  CLUS_2              103                 86
  CLUS_3               34                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       79     24     34     74
  20P GAIN WILD-TYPE     64     30     26     80
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               79                 64
  CLUS_2               24                 30
  CLUS_3               34                 26
  CLUS_4               74                 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
  20P GAIN MUTATED       32     67     57
  20P GAIN WILD-TYPE     47     41     56
D36V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               32                 47
  CLUS_2               67                 41
  CLUS_3               57                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       68     38     50
  20P GAIN WILD-TYPE     78     21     45
D36V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               68                 78
  CLUS_2               38                 21
  CLUS_3               50                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       70     90     69
  20P GAIN WILD-TYPE     51     92     75
D36V11, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               70                 51
  CLUS_2               90                 92
  CLUS_3               69                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED       40     41     98     50
  20P GAIN WILD-TYPE     65     30     67     56
D36V12, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               40                 65
  CLUS_2               41                 30
  CLUS_3               98                 67
  CLUS_4               50                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                    cls
clus                 0 1
  20P GAIN MUTATED   4 6
  20P GAIN WILD-TYPE 8 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4    6
  20P GAIN WILD-TYPE    8    4
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                6                  4
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P GAIN MUTATED        3      0      0      3      3      1
  20P GAIN WILD-TYPE      3      2      2      3      1      1
D36V14, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                3                  3
  CLUS_5                3                  1
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED      143     95     76
  20Q GAIN WILD-TYPE     72    121     50
D37V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              143                 72
  CLUS_2               95                121
  CLUS_3               76                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED      164     83     67
  20Q GAIN WILD-TYPE    146     75     22
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              164                146
  CLUS_2               83                 75
  CLUS_3               67                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       85     95    133
  20Q GAIN WILD-TYPE     74     69     99
D37V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               85                 74
  CLUS_2               95                 69
  CLUS_3              133                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q GAIN MUTATED       35      30     35     40     24     41     26     21
  20Q GAIN WILD-TYPE     50      27     23     42     10     34      8     15
                    vv
clus                 CLUS_8 CLUS_9
  20Q GAIN MUTATED       42     19
  20Q GAIN WILD-TYPE     10     23
D37V4, multiclass
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                35                 50
  CLUS_10               30                 27
  CLUS_2                35                 23
  CLUS_3                40                 42
  CLUS_4                24                 10
  CLUS_5                41                 34
  CLUS_6                26                  8
  CLUS_7                21                 15
  CLUS_8                42                 10
  CLUS_9                19                 23
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       69     98    161
  20Q GAIN WILD-TYPE    102    108     41
D37V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               69                102
  CLUS_2               98                108
  CLUS_3              161                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      132     87    101
  20Q GAIN WILD-TYPE     40     88    120
D37V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              132                 40
  CLUS_2               87                 88
  CLUS_3              101                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
  20Q GAIN MUTATED       83    109     38
  20Q GAIN WILD-TYPE     63     80     38
D37V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               83                 63
  CLUS_2              109                 80
  CLUS_3               38                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       86     26     39     79
  20Q GAIN WILD-TYPE     57     28     21     75
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               86                 57
  CLUS_2               26                 28
  CLUS_3               39                 21
  CLUS_4               79                 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
  20Q GAIN MUTATED       39     71     65
  20Q GAIN WILD-TYPE     40     37     48
D37V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               39                 40
  CLUS_2               71                 37
  CLUS_3               65                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       74     44     57
  20Q GAIN WILD-TYPE     72     15     38
D37V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               74                 72
  CLUS_2               44                 15
  CLUS_3               57                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       78    102     80
  20Q GAIN WILD-TYPE     43     80     64
D37V11, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               78                 43
  CLUS_2              102                 80
  CLUS_3               80                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED       48     47    108     57
  20Q GAIN WILD-TYPE     57     24     57     49
D37V12, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               48                 57
  CLUS_2               47                 24
  CLUS_3              108                 57
  CLUS_4               57                 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"
D37V13, binary
                    cls
clus                 0 1
  20Q GAIN MUTATED   6 5
  20Q GAIN WILD-TYPE 6 5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    5
  20Q GAIN WILD-TYPE    6    5
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                  6
  CLUS_2                5                  5
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q GAIN MUTATED        4      0      0      3      3      1
  20Q GAIN WILD-TYPE      2      2      2      3      1      1
D37V14, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                  2
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                3                  3
  CLUS_5                3                  1
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       39     37     30
  21Q GAIN WILD-TYPE    176    179     96
D38V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               39                176
  CLUS_2               37                179
  CLUS_3               30                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       57     32     17
  21Q GAIN WILD-TYPE    253    126     72
D38V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               57                253
  CLUS_2               32                126
  CLUS_3               17                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       29     31     45
  21Q GAIN WILD-TYPE    130    133    187
D38V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               29                130
  CLUS_2               31                133
  CLUS_3               45                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  21Q GAIN MUTATED       13      11     13     13     10     15     10      5
  21Q GAIN WILD-TYPE     72      46     45     69     24     60     24     31
                    vv
clus                 CLUS_8 CLUS_9
  21Q GAIN MUTATED        8      7
  21Q GAIN WILD-TYPE     44     35
D38V4, multiclass
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                13                 72
  CLUS_10               11                 46
  CLUS_2                13                 45
  CLUS_3                13                 69
  CLUS_4                10                 24
  CLUS_5                15                 60
  CLUS_6                10                 24
  CLUS_7                 5                 31
  CLUS_8                 8                 44
  CLUS_9                 7                 35
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       22     33     54
  21Q GAIN WILD-TYPE    149    173    148
D38V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               22                149
  CLUS_2               33                173
  CLUS_3               54                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
  21Q GAIN MUTATED       45     25     39
  21Q GAIN WILD-TYPE    127    150    182
D38V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               45                127
  CLUS_2               25                150
  CLUS_3               39                182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       27     41      9
  21Q GAIN WILD-TYPE    119    148     67
D38V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               27                119
  CLUS_2               41                148
  CLUS_3                9                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED       26      8     16     27
  21Q GAIN WILD-TYPE    117     46     44    127
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               26                117
  CLUS_2                8                 46
  CLUS_3               16                 44
  CLUS_4               27                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        9     19     24
  21Q GAIN WILD-TYPE     70     89     89
D38V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                9                 70
  CLUS_2               19                 89
  CLUS_3               24                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       19     13     20
  21Q GAIN WILD-TYPE    127     46     75
D38V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               19                127
  CLUS_2               13                 46
  CLUS_3               20                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       34     30     23
  21Q GAIN WILD-TYPE     87    152    121
D38V11, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               34                 87
  CLUS_2               30                152
  CLUS_3               23                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
  21Q GAIN MUTATED       16     20     37     14
  21Q GAIN WILD-TYPE     89     51    128     92
D38V12, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               16                 89
  CLUS_2               20                 51
  CLUS_3               37                128
  CLUS_4               14                 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"
D38V13, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  1
  21Q GAIN WILD-TYPE 11  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    1
  21Q GAIN WILD-TYPE   11    9
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q GAIN MUTATED        0      0      0      0      2      0
  21Q GAIN WILD-TYPE      6      2      2      6      2      2
D38V14, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-2036 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-24-2288         TCGA-24-2289         TCGA-24-2290 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-24-2297         TCGA-25-2392         TCGA-25-2399 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-25-2400         TCGA-25-2404         TCGA-57-1994 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-59-2363         TCGA-61-1918         TCGA-61-2088 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-61-2098         TCGA-61-2109 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        6     11      7
  22Q GAIN WILD-TYPE    209    205    119
D39V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                209
  CLUS_2               11                205
  CLUS_3                7                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
  22Q GAIN MUTATED       14      8      2
  22Q GAIN WILD-TYPE    296    150     87
D39V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               14                296
  CLUS_2                8                150
  CLUS_3                2                 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
  22Q GAIN MUTATED        6      8     10
  22Q GAIN WILD-TYPE    153    156    222
D39V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                153
  CLUS_2                8                156
  CLUS_3               10                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  22Q GAIN MUTATED        4       3      3      3      1      7      1      1
  22Q GAIN WILD-TYPE     81      54     55     79     33     68     33     35
                    vv
clus                 CLUS_8 CLUS_9
  22Q GAIN MUTATED        0      1
  22Q GAIN WILD-TYPE     52     41
D39V4, multiclass
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                 4                 81
  CLUS_10                3                 54
  CLUS_2                 3                 55
  CLUS_3                 3                 79
  CLUS_4                 1                 33
  CLUS_5                 7                 68
  CLUS_6                 1                 33
  CLUS_7                 1                 35
  CLUS_8                 0                 52
  CLUS_9                 1                 41
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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        5     12      7
  22Q GAIN WILD-TYPE    166    194    195
D39V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                166
  CLUS_2               12                194
  CLUS_3                7                195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        5      5     14
  22Q GAIN WILD-TYPE    167    170    207
D39V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                167
  CLUS_2                5                170
  CLUS_3               14                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        6      7      5
  22Q GAIN WILD-TYPE    140    182     71
D39V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                140
  CLUS_2                7                182
  CLUS_3                5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      5      3      3
  22Q GAIN WILD-TYPE    136     49     57    151
D39V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                136
  CLUS_2                5                 49
  CLUS_3                3                 57
  CLUS_4                3                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        1      4      9
  22Q GAIN WILD-TYPE     78    104    104
D39V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 78
  CLUS_2                4                104
  CLUS_3                9                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        6      1      7
  22Q GAIN WILD-TYPE    140     58     88
D39V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                140
  CLUS_2                1                 58
  CLUS_3                7                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        9      7      3
  22Q GAIN WILD-TYPE    112    175    141
D39V11, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                9                112
  CLUS_2                7                175
  CLUS_3                3                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
  22Q GAIN MUTATED        5      0     11      3
  22Q GAIN WILD-TYPE    100     71    154    103
D39V12, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                100
  CLUS_2                0                 71
  CLUS_3               11                154
  CLUS_4                3                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"
D39V13, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1  2
  22Q GAIN WILD-TYPE 11  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    2
  22Q GAIN WILD-TYPE   11    8
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q GAIN MUTATED        0      0      0      1      2      0
  22Q GAIN WILD-TYPE      6      2      2      5      2      2
D39V14, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                1                  5
  CLUS_5                2                  2
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       25     34     17
  XP GAIN WILD-TYPE    190    182    109
D40V1, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              25               190
  CLUS_2              34               182
  CLUS_3              17               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       39     25     12
  XP GAIN WILD-TYPE    271    133     77
D40V2, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              39               271
  CLUS_2              25               133
  CLUS_3              12                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       23     21     31
  XP GAIN WILD-TYPE    136    143    201
D40V3, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              23               136
  CLUS_2              21               143
  CLUS_3              31               201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XP GAIN MUTATED       10       6      8     11      2     14      3      7
  XP GAIN WILD-TYPE     75      51     50     71     32     61     31     29
                   vv
clus                CLUS_8 CLUS_9
  XP GAIN MUTATED       10      4
  XP GAIN WILD-TYPE     42     38
D40V4, multiclass
         clus
vv        XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               10                75
  CLUS_10               6                51
  CLUS_2                8                50
  CLUS_3               11                71
  CLUS_4                2                32
  CLUS_5               14                61
  CLUS_6                3                31
  CLUS_7                7                29
  CLUS_8               10                42
  CLUS_9                4                38
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       14     29     35
  XP GAIN WILD-TYPE    157    177    167
D40V5, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              14               157
  CLUS_2              29               177
  CLUS_3              35               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
  XP GAIN MUTATED       26     25     25
  XP GAIN WILD-TYPE    146    150    196
D40V6, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              26               146
  CLUS_2              25               150
  CLUS_3              25               196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       18     25     12
  XP GAIN WILD-TYPE    128    164     64
D40V7, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              18               128
  CLUS_2              25               164
  CLUS_3              12                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP GAIN MUTATED       15     11      7     22
  XP GAIN WILD-TYPE    128     43     53    132
D40V8, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              15               128
  CLUS_2              11                43
  CLUS_3               7                53
  CLUS_4              22               132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       11     15     14
  XP GAIN WILD-TYPE     68     93     99
D40V9, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              11                68
  CLUS_2              15                93
  CLUS_3              14                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       20      8     12
  XP GAIN WILD-TYPE    126     51     83
D40V10, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              20               126
  CLUS_2               8                51
  CLUS_3              12                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP GAIN MUTATED       17     31     11
  XP GAIN WILD-TYPE    104    151    133
D40V11, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              17               104
  CLUS_2              31               151
  CLUS_3              11               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
  XP GAIN MUTATED       11     10     30      8
  XP GAIN WILD-TYPE     94     61    135     98
D40V12, multiclass
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1              11                94
  CLUS_2              10                61
  CLUS_3              30               135
  CLUS_4               8                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"
D40V13, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    1  0
  XP GAIN WILD-TYPE 11 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    0
  XP GAIN WILD-TYPE   11   10
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  CLUS_1               1                11
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XP GAIN MUTATED        1      0      0      0      0      0
  XP GAIN WILD-TYPE      5      2      2      6      4      2
D40V14, multiclass
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                21 
       TCGA-04-1652        TCGA-09-2050        TCGA-09-2054        TCGA-13-0908 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-23-2077        TCGA-24-1928        TCGA-24-2036        TCGA-24-2288 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-24-2289        TCGA-24-2290        TCGA-24-2297        TCGA-25-2392 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-25-2399        TCGA-25-2400        TCGA-25-2404        TCGA-57-1994 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-59-2363        TCGA-61-1918        TCGA-61-2088        TCGA-61-2098 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-61-2111 
"XP GAIN WILD-TYPE" 

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       38     45     22
  XQ GAIN WILD-TYPE    177    171    104
D41V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              38               177
  CLUS_2              45               171
  CLUS_3              22               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       57     30     18
  XQ GAIN WILD-TYPE    253    128     71
D41V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              57               253
  CLUS_2              30               128
  CLUS_3              18                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     33     45
  XQ GAIN WILD-TYPE    133    131    187
D41V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              26               133
  CLUS_2              33               131
  CLUS_3              45               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ GAIN MUTATED       12       8     11     15      4     22      3      8
  XQ GAIN WILD-TYPE     73      49     47     67     30     53     31     28
                   vv
clus                CLUS_8 CLUS_9
  XQ GAIN MUTATED       13      8
  XQ GAIN WILD-TYPE     39     34
D41V4, multiclass
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               12                73
  CLUS_10               8                49
  CLUS_2               11                47
  CLUS_3               15                67
  CLUS_4                4                30
  CLUS_5               22                53
  CLUS_6                3                31
  CLUS_7                8                28
  CLUS_8               13                39
  CLUS_9                8                34
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       17     35     56
  XQ GAIN WILD-TYPE    154    171    146
D41V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              17               154
  CLUS_2              35               171
  CLUS_3              56               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
  XQ GAIN MUTATED       33     30     42
  XQ GAIN WILD-TYPE    139    145    179
D41V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              33               139
  CLUS_2              30               145
  CLUS_3              42               179
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       26     44     11
  XQ GAIN WILD-TYPE    120    145     65
D41V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              26               120
  CLUS_2              44               145
  CLUS_3              11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED       19     11     13     38
  XQ GAIN WILD-TYPE    124     43     47    116
D41V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              19               124
  CLUS_2              11                43
  CLUS_3              13                47
  CLUS_4              38               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       15     20     22
  XQ GAIN WILD-TYPE     64     88     91
D41V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              15                64
  CLUS_2              20                88
  CLUS_3              22                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       27     10     20
  XQ GAIN WILD-TYPE    119     49     75
D41V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              27               119
  CLUS_2              10                49
  CLUS_3              20                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       24     40     24
  XQ GAIN WILD-TYPE     97    142    120
D41V11, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              24                97
  CLUS_2              40               142
  CLUS_3              24               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED       18     16     37     17
  XQ GAIN WILD-TYPE     87     55    128     89
D41V12, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              18                87
  CLUS_2              16                55
  CLUS_3              37               128
  CLUS_4              17                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"
D41V13, binary
                   cls
clus                0 1
  XQ GAIN MUTATED   3 1
  XQ GAIN WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    1
  XQ GAIN WILD-TYPE    9    9
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ GAIN MUTATED        3      0      0      1      0      0
  XQ GAIN WILD-TYPE      3      2      2      5      4      2
D41V14, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               0                 4
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       33     16     13
  1P LOSS WILD-TYPE    182    200    113
D42V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              33               182
  CLUS_2              16               200
  CLUS_3              13               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
  1P LOSS MUTATED       31     10     21
  1P LOSS WILD-TYPE    279    148     68
D42V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              31               279
  CLUS_2              10               148
  CLUS_3              21                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       14     18     30
  1P LOSS WILD-TYPE    145    146    202
D42V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              14               145
  CLUS_2              18               146
  CLUS_3              30               202
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1P LOSS MUTATED       10       6      6      6      1      6      8      6
  1P LOSS WILD-TYPE     75      51     52     76     33     69     26     30
                   vv
clus                CLUS_8 CLUS_9
  1P LOSS MUTATED        9      4
  1P LOSS WILD-TYPE     43     38
D42V4, multiclass
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               10                75
  CLUS_10               6                51
  CLUS_2                6                52
  CLUS_3                6                76
  CLUS_4                1                33
  CLUS_5                6                69
  CLUS_6                8                26
  CLUS_7                6                30
  CLUS_8                9                43
  CLUS_9                4                38
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     23     19
  1P LOSS WILD-TYPE    148    183    183
D42V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              23               148
  CLUS_2              23               183
  CLUS_3              19               183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       23     21     19
  1P LOSS WILD-TYPE    149    154    202
D42V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              23               149
  CLUS_2              21               154
  CLUS_3              19               202
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       25     17      8
  1P LOSS WILD-TYPE    121    172     68
D42V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              25               121
  CLUS_2              17               172
  CLUS_3               8                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED       22      4      6     18
  1P LOSS WILD-TYPE    121     50     54    136
D42V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              22               121
  CLUS_2               4                50
  CLUS_3               6                54
  CLUS_4              18               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        8     12     10
  1P LOSS WILD-TYPE     71     96    103
D42V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               8                71
  CLUS_2              12                96
  CLUS_3              10               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
  1P LOSS MUTATED       14      9      7
  1P LOSS WILD-TYPE    132     50     88
D42V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              14               132
  CLUS_2               9                50
  CLUS_3               7                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       12     15     18
  1P LOSS WILD-TYPE    109    167    126
D42V11, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              12               109
  CLUS_2              15               167
  CLUS_3              18               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        7     11     16     11
  1P LOSS WILD-TYPE     98     60    149     95
D42V12, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               7                98
  CLUS_2              11                60
  CLUS_3              16               149
  CLUS_4              11                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"
D42V13, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  0
  1P LOSS WILD-TYPE 11 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    0
  1P LOSS WILD-TYPE   11   10
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P LOSS MUTATED        1      0      0      0      0      0
  1P LOSS WILD-TYPE      5      2      2      6      4      2
D42V14, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                21 
       TCGA-04-1652        TCGA-09-2050        TCGA-09-2054        TCGA-13-0908 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-23-2077        TCGA-24-1928        TCGA-24-2036        TCGA-24-2288 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-24-2289        TCGA-24-2290        TCGA-24-2297        TCGA-25-2392 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-25-2399        TCGA-25-2400        TCGA-25-2404        TCGA-57-1994 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-59-2363        TCGA-61-2088        TCGA-61-2098        TCGA-61-2109 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-61-2111 
"1P LOSS WILD-TYPE" 

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED       21     10      9
  1Q LOSS WILD-TYPE    194    206    117
D43V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              21               194
  CLUS_2              10               206
  CLUS_3               9               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
  1Q LOSS MUTATED       20      7     13
  1Q LOSS WILD-TYPE    290    151     76
D43V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              20               290
  CLUS_2               7               151
  CLUS_3              13                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        7      9     24
  1Q LOSS WILD-TYPE    152    155    208
D43V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               152
  CLUS_2               9               155
  CLUS_3              24               208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  1Q LOSS MUTATED        6       5      3      5      1      4      6      3
  1Q LOSS WILD-TYPE     79      52     55     77     33     71     28     33
                   vv
clus                CLUS_8 CLUS_9
  1Q LOSS MUTATED        5      2
  1Q LOSS WILD-TYPE     47     40
D43V4, multiclass
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1                6                79
  CLUS_10               5                52
  CLUS_2                3                55
  CLUS_3                5                77
  CLUS_4                1                33
  CLUS_5                4                71
  CLUS_6                6                28
  CLUS_7                3                33
  CLUS_8                5                47
  CLUS_9                2                40
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       11     18     14
  1Q LOSS WILD-TYPE    160    188    188
D43V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              11               160
  CLUS_2              18               188
  CLUS_3              14               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       14     15     12
  1Q LOSS WILD-TYPE    158    160    209
D43V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              14               158
  CLUS_2              15               160
  CLUS_3              12               209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED       12     13      6
  1Q LOSS WILD-TYPE    134    176     70
D43V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              12               134
  CLUS_2              13               176
  CLUS_3               6                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED       10      4      5     12
  1Q LOSS WILD-TYPE    133     50     55    142
D43V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              10               133
  CLUS_2               4                50
  CLUS_3               5                55
  CLUS_4              12               142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        3      9      7
  1Q LOSS WILD-TYPE     76     99    106
D43V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                76
  CLUS_2               9                99
  CLUS_3               7               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        9      6      4
  1Q LOSS WILD-TYPE    137     53     91
D43V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               9               137
  CLUS_2               6                53
  CLUS_3               4                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        8     11     10
  1Q LOSS WILD-TYPE    113    171    134
D43V11, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               8               113
  CLUS_2              11               171
  CLUS_3              10               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
  1Q LOSS MUTATED        6      5     12      6
  1Q LOSS WILD-TYPE     99     66    153    100
D43V12, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6                99
  CLUS_2               5                66
  CLUS_3              12               153
  CLUS_4               6               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"
D43V13, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    0  0
  1Q LOSS WILD-TYPE 12 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    0
  1Q LOSS WILD-TYPE   12   10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q LOSS MUTATED        0      0      0      0      0      0
  1Q LOSS WILD-TYPE      6      2      2      6      4      2
D43V14, multiclass

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       20     22     11
  2P LOSS WILD-TYPE    195    194    115
D44V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              20               195
  CLUS_2              22               194
  CLUS_3              11               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
  2P LOSS MUTATED       39     10      4
  2P LOSS WILD-TYPE    271    148     85
D44V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              39               271
  CLUS_2              10               148
  CLUS_3               4                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       14     13     25
  2P LOSS WILD-TYPE    145    151    207
D44V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              14               145
  CLUS_2              13               151
  CLUS_3              25               207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2P LOSS MUTATED        8       4      2      7      3      8      5      7
  2P LOSS WILD-TYPE     77      53     56     75     31     67     29     29
                   vv
clus                CLUS_8 CLUS_9
  2P LOSS MUTATED        4      4
  2P LOSS WILD-TYPE     48     38
D44V4, multiclass
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1                8                77
  CLUS_10               4                53
  CLUS_2                2                56
  CLUS_3                7                75
  CLUS_4                3                31
  CLUS_5                8                67
  CLUS_6                5                29
  CLUS_7                7                29
  CLUS_8                4                48
  CLUS_9                4                38
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       17     21     15
  2P LOSS WILD-TYPE    154    185    187
D44V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              17               154
  CLUS_2              21               185
  CLUS_3              15               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       17     14     22
  2P LOSS WILD-TYPE    155    161    199
D44V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              17               155
  CLUS_2              14               161
  CLUS_3              22               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       12     18      7
  2P LOSS WILD-TYPE    134    171     69
D44V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              12               134
  CLUS_2              18               171
  CLUS_3               7                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED       14      3      4     16
  2P LOSS WILD-TYPE    129     51     56    138
D44V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              14               129
  CLUS_2               3                51
  CLUS_3               4                56
  CLUS_4              16               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED       10      8     10
  2P LOSS WILD-TYPE     69    100    103
D44V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10                69
  CLUS_2               8               100
  CLUS_3              10               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
  2P LOSS MUTATED       15      5      8
  2P LOSS WILD-TYPE    131     54     87
D44V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              15               131
  CLUS_2               5                54
  CLUS_3               8                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
  2P LOSS MUTATED       10     20     16
  2P LOSS WILD-TYPE    111    162    128
D44V11, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              10               111
  CLUS_2              20               162
  CLUS_3              16               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 CLUS_4
  2P LOSS MUTATED       13     10     13     10
  2P LOSS WILD-TYPE     92     61    152     96
D44V12, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1              13                92
  CLUS_2              10                61
  CLUS_3              13               152
  CLUS_4              10                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"
D44V13, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  0
  2P LOSS WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    0
  2P LOSS WILD-TYPE   10   10
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                10
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2P LOSS MUTATED        1      0      0      0      0      1
  2P LOSS WILD-TYPE      5      2      2      6      4      1
D44V14, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                20 
       TCGA-04-1652        TCGA-09-2050        TCGA-09-2054        TCGA-13-0908 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-23-2077        TCGA-24-1928        TCGA-24-2036        TCGA-24-2288 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-24-2289        TCGA-24-2290        TCGA-24-2297        TCGA-25-2399 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-25-2400        TCGA-25-2404        TCGA-57-1994        TCGA-59-2363 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-61-1918        TCGA-61-2088        TCGA-61-2098        TCGA-61-2111 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       21     22     14
  2Q LOSS WILD-TYPE    194    194    112
D45V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              21               194
  CLUS_2              22               194
  CLUS_3              14               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
  2Q LOSS MUTATED       36     16      5
  2Q LOSS WILD-TYPE    274    142     84
D45V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              36               274
  CLUS_2              16               142
  CLUS_3               5                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       15     15     27
  2Q LOSS WILD-TYPE    144    149    205
D45V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              15               144
  CLUS_2              15               149
  CLUS_3              27               205
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  2Q LOSS MUTATED        9       3      2      8      4      7      5      9
  2Q LOSS WILD-TYPE     76      54     56     74     30     68     29     27
                   vv
clus                CLUS_8 CLUS_9
  2Q LOSS MUTATED        5      5
  2Q LOSS WILD-TYPE     47     37
D45V4, multiclass
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1                9                76
  CLUS_10               3                54
  CLUS_2                2                56
  CLUS_3                8                74
  CLUS_4                4                30
  CLUS_5                7                68
  CLUS_6                5                29
  CLUS_7                9                27
  CLUS_8                5                47
  CLUS_9                5                37
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       16     23     20
  2Q LOSS WILD-TYPE    155    183    182
D45V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              16               155
  CLUS_2              23               183
  CLUS_3              20               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       19     15     24
  2Q LOSS WILD-TYPE    153    160    197
D45V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              19               153
  CLUS_2              15               160
  CLUS_3              24               197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       17     21      6
  2Q LOSS WILD-TYPE    129    168     70
D45V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              17               129
  CLUS_2              21               168
  CLUS_3               6                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED       21      2      5     16
  2Q LOSS WILD-TYPE    122     52     55    138
D45V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              21               122
  CLUS_2               2                52
  CLUS_3               5                55
  CLUS_4              16               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       10      7     12
  2Q LOSS WILD-TYPE     69    101    101
D45V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              10                69
  CLUS_2               7               101
  CLUS_3              12               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       15      4     10
  2Q LOSS WILD-TYPE    131     55     85
D45V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              15               131
  CLUS_2               4                55
  CLUS_3              10                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       16     21     13
  2Q LOSS WILD-TYPE    105    161    131
D45V11, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              16               105
  CLUS_2              21               161
  CLUS_3              13               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
  2Q LOSS MUTATED       16      9     18      7
  2Q LOSS WILD-TYPE     89     62    147     99
D45V12, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              16                89
  CLUS_2               9                62
  CLUS_3              18               147
  CLUS_4               7                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"
D45V13, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    2  0
  2Q LOSS WILD-TYPE 10 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    0
  2Q LOSS WILD-TYPE   10   10
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                10
  CLUS_2               0                10
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q LOSS MUTATED        1      0      0      0      0      1
  2Q LOSS WILD-TYPE      5      2      2      6      4      1
D45V14, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                20 
       TCGA-04-1652        TCGA-09-2050        TCGA-09-2054        TCGA-13-0908 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-23-2077        TCGA-24-1928        TCGA-24-2036        TCGA-24-2288 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-24-2289        TCGA-24-2290        TCGA-24-2297        TCGA-25-2399 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-25-2400        TCGA-25-2404        TCGA-57-1994        TCGA-59-2363 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-61-1918        TCGA-61-2088        TCGA-61-2098        TCGA-61-2111 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       45     25     24
  3P LOSS WILD-TYPE    170    191    102
D46V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              45               170
  CLUS_2              25               191
  CLUS_3              24               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       38     30     26
  3P LOSS WILD-TYPE    272    128     63
D46V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              38               272
  CLUS_2              30               128
  CLUS_3              26                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     27     42
  3P LOSS WILD-TYPE    134    137    190
D46V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              25               134
  CLUS_2              27               137
  CLUS_3              42               190
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3P LOSS MUTATED       16       4      4     12      5     13     12      8
  3P LOSS WILD-TYPE     69      53     54     70     29     62     22     28
                   vv
clus                CLUS_8 CLUS_9
  3P LOSS MUTATED       15      5
  3P LOSS WILD-TYPE     37     37
D46V4, multiclass
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               16                69
  CLUS_10               4                53
  CLUS_2                4                54
  CLUS_3               12                70
  CLUS_4                5                29
  CLUS_5               13                62
  CLUS_6               12                22
  CLUS_7                8                28
  CLUS_8               15                37
  CLUS_9                5                37
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       23     22     50
  3P LOSS WILD-TYPE    148    184    152
D46V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              23               148
  CLUS_2              22               184
  CLUS_3              50               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
  3P LOSS MUTATED       42     27     25
  3P LOSS WILD-TYPE    130    148    196
D46V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              42               130
  CLUS_2              27               148
  CLUS_3              25               196
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       23     33      6
  3P LOSS WILD-TYPE    123    156     70
D46V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              23               123
  CLUS_2              33               156
  CLUS_3               6                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED       19      8     17     18
  3P LOSS WILD-TYPE    124     46     43    136
D46V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              19               124
  CLUS_2               8                46
  CLUS_3              17                43
  CLUS_4              18               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        8     22     24
  3P LOSS WILD-TYPE     71     86     89
D46V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               8                71
  CLUS_2              22                86
  CLUS_3              24                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       15     18     21
  3P LOSS WILD-TYPE    131     41     74
D46V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              15               131
  CLUS_2              18                41
  CLUS_3              21                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       28     26     23
  3P LOSS WILD-TYPE     93    156    121
D46V11, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              28                93
  CLUS_2              26               156
  CLUS_3              23               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
  3P LOSS MUTATED       11     15     35     16
  3P LOSS WILD-TYPE     94     56    130     90
D46V12, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              11                94
  CLUS_2              15                56
  CLUS_3              35               130
  CLUS_4              16                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"
D46V13, binary
                   cls
clus                0 1
  3P LOSS MUTATED   3 2
  3P LOSS WILD-TYPE 9 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE    9    8
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P LOSS MUTATED        1      1      0      1      0      2
  3P LOSS WILD-TYPE      5      1      2      5      4      0
D46V14, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               0                 4
  CLUS_6               2                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       22      8     13
  3Q LOSS WILD-TYPE    193    208    113
D47V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              22               193
  CLUS_2               8               208
  CLUS_3              13               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
  3Q LOSS MUTATED       17     14     12
  3Q LOSS WILD-TYPE    293    144     77
D47V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              17               293
  CLUS_2              14               144
  CLUS_3              12                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        9     11     23
  3Q LOSS WILD-TYPE    150    153    209
D47V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               9               150
  CLUS_2              11               153
  CLUS_3              23               209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  3Q LOSS MUTATED        7       1      1      7      2      6      7      3
  3Q LOSS WILD-TYPE     78      56     57     75     32     69     27     33
                   vv
clus                CLUS_8 CLUS_9
  3Q LOSS MUTATED        7      2
  3Q LOSS WILD-TYPE     45     40
D47V4, multiclass
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1                7                78
  CLUS_10               1                56
  CLUS_2                1                57
  CLUS_3                7                75
  CLUS_4                2                32
  CLUS_5                6                69
  CLUS_6                7                27
  CLUS_7                3                33
  CLUS_8                7                45
  CLUS_9                2                40
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       14      8     21
  3Q LOSS WILD-TYPE    157    198    181
D47V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              14               157
  CLUS_2               8               198
  CLUS_3              21               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       22     13      8
  3Q LOSS WILD-TYPE    150    162    213
D47V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              22               150
  CLUS_2              13               162
  CLUS_3               8               213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       12     13      2
  3Q LOSS WILD-TYPE    134    176     74
D47V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              12               134
  CLUS_2              13               176
  CLUS_3               2                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        9      7      5      6
  3Q LOSS WILD-TYPE    134     47     55    148
D47V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               9               134
  CLUS_2               7                47
  CLUS_3               5                55
  CLUS_4               6               148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        2      9     13
  3Q LOSS WILD-TYPE     77     99    100
D47V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                77
  CLUS_2               9                99
  CLUS_3              13               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
  3Q LOSS MUTATED        6      8     10
  3Q LOSS WILD-TYPE    140     51     85
D47V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               6               140
  CLUS_2               8                51
  CLUS_3              10                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       12     14      7
  3Q LOSS WILD-TYPE    109    168    137
D47V11, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              12               109
  CLUS_2              14               168
  CLUS_3               7               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
  3Q LOSS MUTATED        3      7     21      2
  3Q LOSS WILD-TYPE    102     64    144    104
D47V12, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3               102
  CLUS_2               7                64
  CLUS_3              21               144
  CLUS_4               2               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"
D47V13, binary
                   cls
clus                0 1
  3Q LOSS MUTATED   3 1
  3Q LOSS WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    1
  3Q LOSS WILD-TYPE    9    9
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q LOSS MUTATED        1      1      0      0      0      2
  3Q LOSS WILD-TYPE      5      1      2      6      4      0
D47V14, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               0                 6
  CLUS_5               0                 4
  CLUS_6               2                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED      125    112     66
  4P LOSS WILD-TYPE     90    104     60
D48V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1             125                90
  CLUS_2             112               104
  CLUS_3              66                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      176     72     55
  4P LOSS WILD-TYPE    134     86     34
D48V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1             176               134
  CLUS_2              72                86
  CLUS_3              55                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       95     86    121
  4P LOSS WILD-TYPE     64     78    111
D48V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              95                64
  CLUS_2              86                78
  CLUS_3             121               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4P LOSS MUTATED       46      32     34     46     19     35     21     22
  4P LOSS WILD-TYPE     39      25     24     36     15     40     13     14
                   vv
clus                CLUS_8 CLUS_9
  4P LOSS MUTATED       30     17
  4P LOSS WILD-TYPE     22     25
D48V4, multiclass
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               46                39
  CLUS_10              32                25
  CLUS_2               34                24
  CLUS_3               46                36
  CLUS_4               19                15
  CLUS_5               35                40
  CLUS_6               21                13
  CLUS_7               22                14
  CLUS_8               30                22
  CLUS_9               17                25
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       93     96    127
  4P LOSS WILD-TYPE     78    110     75
D48V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              93                78
  CLUS_2              96               110
  CLUS_3             127                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED      101     94    117
  4P LOSS WILD-TYPE     71     81    104
D48V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1             101                71
  CLUS_2              94                81
  CLUS_3             117               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       75    105     32
  4P LOSS WILD-TYPE     71     84     44
D48V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              75                71
  CLUS_2             105                84
  CLUS_3              32                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED       74     25     33     80
  4P LOSS WILD-TYPE     69     29     27     74
D48V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              74                69
  CLUS_2              25                29
  CLUS_3              33                27
  CLUS_4              80                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
  4P LOSS MUTATED       36     59     60
  4P LOSS WILD-TYPE     43     49     53
D48V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              36                43
  CLUS_2              59                49
  CLUS_3              60                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       75     32     48
  4P LOSS WILD-TYPE     71     27     47
D48V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              75                71
  CLUS_2              32                27
  CLUS_3              48                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       57     96     86
  4P LOSS WILD-TYPE     64     86     58
D48V11, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              57                64
  CLUS_2              96                86
  CLUS_3              86                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED       55     34     84     66
  4P LOSS WILD-TYPE     50     37     81     40
D48V12, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              55                50
  CLUS_2              34                37
  CLUS_3              84                81
  CLUS_4              66                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                   cls
clus                0 1
  4P LOSS MUTATED   7 5
  4P LOSS WILD-TYPE 5 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7    5
  4P LOSS WILD-TYPE    5    5
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7                 5
  CLUS_2               5                 5
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P LOSS MUTATED        4      2      0      3      2      1
  4P LOSS WILD-TYPE      2      0      2      3      2      1
D48V14, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               2                 0
  CLUS_3               0                 2
  CLUS_4               3                 3
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED      143    127     75
  4Q LOSS WILD-TYPE     72     89     51
D49V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1             143                72
  CLUS_2             127                89
  CLUS_3              75                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED      195     88     62
  4Q LOSS WILD-TYPE    115     70     27
D49V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1             195               115
  CLUS_2              88                70
  CLUS_3              62                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      104     97    143
  4Q LOSS WILD-TYPE     55     67     89
D49V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1             104                55
  CLUS_2              97                67
  CLUS_3             143                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  4Q LOSS MUTATED       54      37     38     51     18     44     23     22
  4Q LOSS WILD-TYPE     31      20     20     31     16     31     11     14
                   vv
clus                CLUS_8 CLUS_9
  4Q LOSS MUTATED       36     21
  4Q LOSS WILD-TYPE     16     21
D49V4, multiclass
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               54                31
  CLUS_10              37                20
  CLUS_2               38                20
  CLUS_3               51                31
  CLUS_4               18                16
  CLUS_5               44                31
  CLUS_6               23                11
  CLUS_7               22                14
  CLUS_8               36                16
  CLUS_9               21                21
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      107    111    144
  4Q LOSS WILD-TYPE     64     95     58
D49V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1             107                64
  CLUS_2             111                95
  CLUS_3             144                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED      113    107    134
  4Q LOSS WILD-TYPE     59     68     87
D49V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1             113                59
  CLUS_2             107                68
  CLUS_3             134                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
  4Q LOSS MUTATED       87    126     43
  4Q LOSS WILD-TYPE     59     63     33
D49V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              87                59
  CLUS_2             126                63
  CLUS_3              43                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       85     30     36    105
  4Q LOSS WILD-TYPE     58     24     24     49
D49V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              85                58
  CLUS_2              30                24
  CLUS_3              36                24
  CLUS_4             105                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
  4Q LOSS MUTATED       49     71     68
  4Q LOSS WILD-TYPE     30     37     45
D49V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              49                30
  CLUS_2              71                37
  CLUS_3              68                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED       90     41     57
  4Q LOSS WILD-TYPE     56     18     38
D49V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              90                56
  CLUS_2              41                18
  CLUS_3              57                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       68    112     96
  4Q LOSS WILD-TYPE     53     70     48
D49V11, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              68                53
  CLUS_2             112                70
  CLUS_3              96                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED       61     42     98     75
  4Q LOSS WILD-TYPE     44     29     67     31
D49V12, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              61                44
  CLUS_2              42                29
  CLUS_3              98                67
  CLUS_4              75                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                   cls
clus                0 1
  4Q LOSS MUTATED   9 7
  4Q LOSS WILD-TYPE 3 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    7
  4Q LOSS WILD-TYPE    3    3
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9                 3
  CLUS_2               7                 3
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q LOSS MUTATED        5      2      0      4      3      2
  4Q LOSS WILD-TYPE      1      0      2      2      1      0
D49V14, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                 1
  CLUS_2               2                 0
  CLUS_3               0                 2
  CLUS_4               4                 2
  CLUS_5               3                 1
  CLUS_6               2                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       61     44     24
  5P LOSS WILD-TYPE    154    172    102
D50V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              61               154
  CLUS_2              44               172
  CLUS_3              24               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       69     30     30
  5P LOSS WILD-TYPE    241    128     59
D50V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              69               241
  CLUS_2              30               128
  CLUS_3              30                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       36     43     50
  5P LOSS WILD-TYPE    123    121    182
D50V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              36               123
  CLUS_2              43               121
  CLUS_3              50               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5P LOSS MUTATED       17      12     13     17      4     15     11      9
  5P LOSS WILD-TYPE     68      45     45     65     30     60     23     27
                   vv
clus                CLUS_8 CLUS_9
  5P LOSS MUTATED       22      9
  5P LOSS WILD-TYPE     30     33
D50V4, multiclass
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               17                68
  CLUS_10              12                45
  CLUS_2               13                45
  CLUS_3               17                65
  CLUS_4                4                30
  CLUS_5               15                60
  CLUS_6               11                23
  CLUS_7                9                27
  CLUS_8               22                30
  CLUS_9                9                33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       33     39     61
  5P LOSS WILD-TYPE    138    167    141
D50V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              33               138
  CLUS_2              39               167
  CLUS_3              61               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
  5P LOSS MUTATED       52     28     50
  5P LOSS WILD-TYPE    120    147    171
D50V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              52               120
  CLUS_2              28               147
  CLUS_3              50               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
  5P LOSS MUTATED       26     50     13
  5P LOSS WILD-TYPE    120    139     63
D50V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              26               120
  CLUS_2              50               139
  CLUS_3              13                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED       26     10     11     42
  5P LOSS WILD-TYPE    117     44     49    112
D50V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              26               117
  CLUS_2              10                44
  CLUS_3              11                49
  CLUS_4              42               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       13     42     23
  5P LOSS WILD-TYPE     66     66     90
D50V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              13                66
  CLUS_2              42                66
  CLUS_3              23                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       35     26     17
  5P LOSS WILD-TYPE    111     33     78
D50V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              35               111
  CLUS_2              26                33
  CLUS_3              17                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       28     42     40
  5P LOSS WILD-TYPE     93    140    104
D50V11, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              28                93
  CLUS_2              42               140
  CLUS_3              40               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED       23     27     38     22
  5P LOSS WILD-TYPE     82     44    127     84
D50V12, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              23                82
  CLUS_2              27                44
  CLUS_3              38               127
  CLUS_4              22                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"
D50V13, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  1
  5P LOSS WILD-TYPE 10  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    1
  5P LOSS WILD-TYPE   10    9
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                10
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P LOSS MUTATED        1      0      0      2      0      0
  5P LOSS WILD-TYPE      5      2      2      4      4      2
D50V14, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               0                 4
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED      105     68     41
  5Q LOSS WILD-TYPE    110    148     85
D51V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1             105               110
  CLUS_2              68               148
  CLUS_3              41                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      113     52     49
  5Q LOSS WILD-TYPE    197    106     40
D51V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1             113               197
  CLUS_2              52               106
  CLUS_3              49                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       58     62     94
  5Q LOSS WILD-TYPE    101    102    138
D51V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              58               101
  CLUS_2              62               102
  CLUS_3              94               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"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  5Q LOSS MUTATED       27      20     23     28     14     24     22     14
  5Q LOSS WILD-TYPE     58      37     35     54     20     51     12     22
                   vv
clus                CLUS_8 CLUS_9
  5Q LOSS MUTATED       29     13
  5Q LOSS WILD-TYPE     23     29
D51V4, multiclass
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               27                58
  CLUS_10              20                37
  CLUS_2               23                35
  CLUS_3               28                54
  CLUS_4               14                20
  CLUS_5               24                51
  CLUS_6               22                12
  CLUS_7               14                22
  CLUS_8               29                23
  CLUS_9               13                29
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     69    100
  5Q LOSS WILD-TYPE    117    137    102
D51V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              54               117
  CLUS_2              69               137
  CLUS_3             100               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       96     51     72
  5Q LOSS WILD-TYPE     76    124    149
D51V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              96                76
  CLUS_2              51               124
  CLUS_3              72               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
  5Q LOSS MUTATED       51     79     21
  5Q LOSS WILD-TYPE     95    110     55
D51V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              51                95
  CLUS_2              79               110
  CLUS_3              21                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED       47     19     21     64
  5Q LOSS WILD-TYPE     96     35     39     90
D51V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              47                96
  CLUS_2              19                35
  CLUS_3              21                39
  CLUS_4              64                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
  5Q LOSS MUTATED       24     58     37
  5Q LOSS WILD-TYPE     55     50     76
D51V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              24                55
  CLUS_2              58                50
  CLUS_3              37                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       55     35     29
  5Q LOSS WILD-TYPE     91     24     66
D51V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              55                91
  CLUS_2              35                24
  CLUS_3              29                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       48     78     54
  5Q LOSS WILD-TYPE     73    104     90
D51V11, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              48                73
  CLUS_2              78               104
  CLUS_3              54                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED       37     36     76     31
  5Q LOSS WILD-TYPE     68     35     89     75
D51V12, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              37                68
  CLUS_2              36                35
  CLUS_3              76                89
  CLUS_4              31                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"
D51V13, binary
                   cls
clus                0 1
  5Q LOSS MUTATED   3 5
  5Q LOSS WILD-TYPE 9 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    5
  5Q LOSS WILD-TYPE    9    5
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               5                 5
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q LOSS MUTATED        3      1      0      3      1      0
  5Q LOSS WILD-TYPE      3      1      2      3      3      2
D51V14, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                 3
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               3                 3
  CLUS_5               1                 3
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       61     63     35
  6P LOSS WILD-TYPE    154    153     91
D52V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              61               154
  CLUS_2              63               153
  CLUS_3              35                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       98     46     15
  6P LOSS WILD-TYPE    212    112     74
D52V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              98               212
  CLUS_2              46               112
  CLUS_3              15                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       52     45     63
  6P LOSS WILD-TYPE    107    119    169
D52V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              52               107
  CLUS_2              45               119
  CLUS_3              63               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6P LOSS MUTATED       28      18     18     21     10     23     11     13
  6P LOSS WILD-TYPE     57      39     40     61     24     52     23     23
                   vv
clus                CLUS_8 CLUS_9
  6P LOSS MUTATED        8     10
  6P LOSS WILD-TYPE     44     32
D52V4, multiclass
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               28                57
  CLUS_10              18                39
  CLUS_2               18                40
  CLUS_3               21                61
  CLUS_4               10                24
  CLUS_5               23                52
  CLUS_6               11                23
  CLUS_7               13                23
  CLUS_8                8                44
  CLUS_9               10                32
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       58     57     50
  6P LOSS WILD-TYPE    113    149    152
D52V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              58               113
  CLUS_2              57               149
  CLUS_3              50               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
  6P LOSS MUTATED       40     58     65
  6P LOSS WILD-TYPE    132    117    156
D52V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              40               132
  CLUS_2              58               117
  CLUS_3              65               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
  6P LOSS MUTATED       37     58     21
  6P LOSS WILD-TYPE    109    131     55
D52V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              37               109
  CLUS_2              58               131
  CLUS_3              21                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED       42     11     18     45
  6P LOSS WILD-TYPE    101     43     42    109
D52V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              42               101
  CLUS_2              11                43
  CLUS_3              18                42
  CLUS_4              45               109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       22     25     34
  6P LOSS WILD-TYPE     57     83     79
D52V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              22                57
  CLUS_2              25                83
  CLUS_3              34                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       44      9     28
  6P LOSS WILD-TYPE    102     50     67
D52V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              44               102
  CLUS_2               9                50
  CLUS_3              28                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       31     58     40
  6P LOSS WILD-TYPE     90    124    104
D52V11, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              31                90
  CLUS_2              58               124
  CLUS_3              40               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED       33     12     51     33
  6P LOSS WILD-TYPE     72     59    114     73
D52V12, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              33                72
  CLUS_2              12                59
  CLUS_3              51               114
  CLUS_4              33                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"
D52V13, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    1  2
  6P LOSS WILD-TYPE 11  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    2
  6P LOSS WILD-TYPE   11    8
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P LOSS MUTATED        0      0      1      1      1      0
  6P LOSS WILD-TYPE      6      2      1      5      3      2
D52V14, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               0                 2
  CLUS_3               1                 1
  CLUS_4               1                 5
  CLUS_5               1                 3
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       89     91     54
  6Q LOSS WILD-TYPE    126    125     72
D53V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              89               126
  CLUS_2              91               125
  CLUS_3              54                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED      134     72     28
  6Q LOSS WILD-TYPE    176     86     61
D53V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1             134               176
  CLUS_2              72                86
  CLUS_3              28                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       70     74     91
  6Q LOSS WILD-TYPE     89     90    141
D53V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              70                89
  CLUS_2              74                90
  CLUS_3              91               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  6Q LOSS MUTATED       39      29     27     29     11     39     15     17
  6Q LOSS WILD-TYPE     46      28     31     53     23     36     19     19
                   vv
clus                CLUS_8 CLUS_9
  6Q LOSS MUTATED       14     15
  6Q LOSS WILD-TYPE     38     27
D53V4, multiclass
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               39                46
  CLUS_10              29                28
  CLUS_2               27                31
  CLUS_3               29                53
  CLUS_4               11                23
  CLUS_5               39                36
  CLUS_6               15                19
  CLUS_7               17                19
  CLUS_8               14                38
  CLUS_9               15                27
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       80     92     70
  6Q LOSS WILD-TYPE     91    114    132
D53V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              80                91
  CLUS_2              92               114
  CLUS_3              70               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
  6Q LOSS MUTATED       60     80     99
  6Q LOSS WILD-TYPE    112     95    122
D53V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              60               112
  CLUS_2              80                95
  CLUS_3              99               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
  6Q LOSS MUTATED       56     81     30
  6Q LOSS WILD-TYPE     90    108     46
D53V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              56                90
  CLUS_2              81               108
  CLUS_3              30                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       61     22     26     58
  6Q LOSS WILD-TYPE     82     32     34     96
D53V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              61                82
  CLUS_2              22                32
  CLUS_3              26                34
  CLUS_4              58                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
  6Q LOSS MUTATED       32     36     54
  6Q LOSS WILD-TYPE     47     72     59
D53V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              32                47
  CLUS_2              36                72
  CLUS_3              54                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       60     15     47
  6Q LOSS WILD-TYPE     86     44     48
D53V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              60                86
  CLUS_2              15                44
  CLUS_3              47                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       48     75     63
  6Q LOSS WILD-TYPE     73    107     81
D53V11, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              48                73
  CLUS_2              75               107
  CLUS_3              63                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED       47     25     67     47
  6Q LOSS WILD-TYPE     58     46     98     59
D53V12, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              47                58
  CLUS_2              25                46
  CLUS_3              67                98
  CLUS_4              47                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"
D53V13, binary
                   cls
clus                0 1
  6Q LOSS MUTATED   3 1
  6Q LOSS WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3    1
  6Q LOSS WILD-TYPE    9    9
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q LOSS MUTATED        1      0      1      1      1      0
  6Q LOSS WILD-TYPE      5      2      1      5      3      2
D53V14, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               0                 2
  CLUS_3               1                 1
  CLUS_4               1                 5
  CLUS_5               1                 3
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       45     45     27
  7P LOSS WILD-TYPE    170    171     99
D54V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              45               170
  CLUS_2              45               171
  CLUS_3              27                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       60     39     18
  7P LOSS WILD-TYPE    250    119     71
D54V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              60               250
  CLUS_2              39               119
  CLUS_3              18                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       32     40     45
  7P LOSS WILD-TYPE    127    124    187
D54V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              32               127
  CLUS_2              40               124
  CLUS_3              45               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7P LOSS MUTATED       16      13     14     17      7     14      4      8
  7P LOSS WILD-TYPE     69      44     44     65     27     61     30     28
                   vv
clus                CLUS_8 CLUS_9
  7P LOSS MUTATED       10     14
  7P LOSS WILD-TYPE     42     28
D54V4, multiclass
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               16                69
  CLUS_10              13                44
  CLUS_2               14                44
  CLUS_3               17                65
  CLUS_4                7                27
  CLUS_5               14                61
  CLUS_6                4                30
  CLUS_7                8                28
  CLUS_8               10                42
  CLUS_9               14                28
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       31     53     37
  7P LOSS WILD-TYPE    140    153    165
D54V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              31               140
  CLUS_2              53               153
  CLUS_3              37               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
  7P LOSS MUTATED       35     45     39
  7P LOSS WILD-TYPE    137    130    182
D54V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              35               137
  CLUS_2              45               130
  CLUS_3              39               182
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       27     45     16
  7P LOSS WILD-TYPE    119    144     60
D54V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              27               119
  CLUS_2              45               144
  CLUS_3              16                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       30     13     14     31
  7P LOSS WILD-TYPE    113     41     46    123
D54V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              30               113
  CLUS_2              13                41
  CLUS_3              14                46
  CLUS_4              31               123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       14     29     35
  7P LOSS WILD-TYPE     65     79     78
D54V9, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              14                65
  CLUS_2              29                79
  CLUS_3              35                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       32     16     30
  7P LOSS WILD-TYPE    114     43     65
D54V10, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              32               114
  CLUS_2              16                43
  CLUS_3              30                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       31     37     31
  7P LOSS WILD-TYPE     90    145    113
D54V11, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              31                90
  CLUS_2              37               145
  CLUS_3              31               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
  7P LOSS MUTATED       26     13     36     24
  7P LOSS WILD-TYPE     79     58    129     82
D54V12, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              26                79
  CLUS_2              13                58
  CLUS_3              36               129
  CLUS_4              24                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"
D54V13, binary
                   cls
clus                0 1
  7P LOSS MUTATED   3 1
  7P LOSS WILD-TYPE 9 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    1
  7P LOSS WILD-TYPE    9    9
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P LOSS MUTATED        0      0      1      2      0      1
  7P LOSS WILD-TYPE      6      2      1      4      4      1
D54V14, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               0                 2
  CLUS_3               1                 1
  CLUS_4               2                 4
  CLUS_5               0                 4
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       31     27     23
  7Q LOSS WILD-TYPE    184    189    103
D55V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              31               184
  CLUS_2              27               189
  CLUS_3              23               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
  7Q LOSS MUTATED       37     31     13
  7Q LOSS WILD-TYPE    273    127     76
D55V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              37               273
  CLUS_2              31               127
  CLUS_3              13                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       19     29     33
  7Q LOSS WILD-TYPE    140    135    199
D55V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              19               140
  CLUS_2              29               135
  CLUS_3              33               199
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  7Q LOSS MUTATED        9       9     10     10      5     13      1      4
  7Q LOSS WILD-TYPE     76      48     48     72     29     62     33     32
                   vv
clus                CLUS_8 CLUS_9
  7Q LOSS MUTATED       10     10
  7Q LOSS WILD-TYPE     42     32
D55V4, multiclass
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1                9                76
  CLUS_10               9                48
  CLUS_2               10                48
  CLUS_3               10                72
  CLUS_4                5                29
  CLUS_5               13                62
  CLUS_6                1                33
  CLUS_7                4                32
  CLUS_8               10                42
  CLUS_9               10                32
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     32     27
  7Q LOSS WILD-TYPE    149    174    175
D55V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              22               149
  CLUS_2              32               174
  CLUS_3              27               175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       25     32     24
  7Q LOSS WILD-TYPE    147    143    197
D55V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              25               147
  CLUS_2              32               143
  CLUS_3              24               197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       21     28     11
  7Q LOSS WILD-TYPE    125    161     65
D55V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              21               125
  CLUS_2              28               161
  CLUS_3              11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED       21      9     12     18
  7Q LOSS WILD-TYPE    122     45     48    136
D55V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              21               122
  CLUS_2               9                45
  CLUS_3              12                48
  CLUS_4              18               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       11     22     26
  7Q LOSS WILD-TYPE     68     86     87
D55V9, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              11                68
  CLUS_2              22                86
  CLUS_3              26                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
  7Q LOSS MUTATED       21     13     25
  7Q LOSS WILD-TYPE    125     46     70
D55V10, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              21               125
  CLUS_2              13                46
  CLUS_3              25                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       25     22     24
  7Q LOSS WILD-TYPE     96    160    120
D55V11, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              25                96
  CLUS_2              22               160
  CLUS_3              24               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED       14     12     29     16
  7Q LOSS WILD-TYPE     91     59    136     90
D55V12, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              14                91
  CLUS_2              12                59
  CLUS_3              29               136
  CLUS_4              16                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"
D55V13, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    2  1
  7Q LOSS WILD-TYPE 10  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE   10    9
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2                10
  CLUS_2               1                 9
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q LOSS MUTATED        0      0      0      2      0      1
  7Q LOSS WILD-TYPE      6      2      2      4      4      1
D55V14, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               0                 2
  CLUS_3               0                 2
  CLUS_4               2                 4
  CLUS_5               0                 4
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED      105     98     61
  8P LOSS WILD-TYPE    110    118     65
D56V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1             105               110
  CLUS_2              98               118
  CLUS_3              61                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED      144     77     43
  8P LOSS WILD-TYPE    166     81     46
D56V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1             144               166
  CLUS_2              77                81
  CLUS_3              43                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     87    104
  8P LOSS WILD-TYPE     86     77    128
D56V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              73                86
  CLUS_2              87                77
  CLUS_3             104               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8P LOSS MUTATED       40      25     28     35     19     39     14     18
  8P LOSS WILD-TYPE     45      32     30     47     15     36     20     18
                   vv
clus                CLUS_8 CLUS_9
  8P LOSS MUTATED       26     20
  8P LOSS WILD-TYPE     26     22
D56V4, multiclass
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               40                45
  CLUS_10              25                32
  CLUS_2               28                30
  CLUS_3               35                47
  CLUS_4               19                15
  CLUS_5               39                36
  CLUS_6               14                20
  CLUS_7               18                18
  CLUS_8               26                26
  CLUS_9               20                22
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       66     97    114
  8P LOSS WILD-TYPE    105    109     88
D56V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              66               105
  CLUS_2              97               109
  CLUS_3             114                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       91     73    107
  8P LOSS WILD-TYPE     81    102    114
D56V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              91                81
  CLUS_2              73               102
  CLUS_3             107               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
  8P LOSS MUTATED       72    101     28
  8P LOSS WILD-TYPE     74     88     48
D56V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              72                74
  CLUS_2             101                88
  CLUS_3              28                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED       74     22     32     73
  8P LOSS WILD-TYPE     69     32     28     81
D56V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              74                69
  CLUS_2              22                32
  CLUS_3              32                28
  CLUS_4              73                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       38     57     56
  8P LOSS WILD-TYPE     41     51     57
D56V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              38                41
  CLUS_2              57                51
  CLUS_3              56                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       74     32     45
  8P LOSS WILD-TYPE     72     27     50
D56V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              74                72
  CLUS_2              32                27
  CLUS_3              45                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       59     81     70
  8P LOSS WILD-TYPE     62    101     74
D56V11, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              59                62
  CLUS_2              81               101
  CLUS_3              70                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED       37     39     83     51
  8P LOSS WILD-TYPE     68     32     82     55
D56V12, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              37                68
  CLUS_2              39                32
  CLUS_3              83                82
  CLUS_4              51                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"
D56V13, binary
                   cls
clus                0 1
  8P LOSS MUTATED   7 6
  8P LOSS WILD-TYPE 5 4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7    6
  8P LOSS WILD-TYPE    5    4
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7                 5
  CLUS_2               6                 4
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P LOSS MUTATED        4      2      1      3      2      1
  8P LOSS WILD-TYPE      2      0      1      3      2      1
D56V14, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               2                 0
  CLUS_3               1                 1
  CLUS_4               3                 3
  CLUS_5               2                 2
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       46     25     14
  8Q LOSS WILD-TYPE    169    191    112
D57V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              46               169
  CLUS_2              25               191
  CLUS_3              14               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
  8Q LOSS MUTATED       43     18     24
  8Q LOSS WILD-TYPE    267    140     65
D57V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              43               267
  CLUS_2              18               140
  CLUS_3              24                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       20     27     38
  8Q LOSS WILD-TYPE    139    137    194
D57V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              20               139
  CLUS_2              27               137
  CLUS_3              38               194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  8Q LOSS MUTATED       11       5     13     10      4      9      6      6
  8Q LOSS WILD-TYPE     74      52     45     72     30     66     28     30
                   vv
clus                CLUS_8 CLUS_9
  8Q LOSS MUTATED       14      7
  8Q LOSS WILD-TYPE     38     35
D57V4, multiclass
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               11                74
  CLUS_10               5                52
  CLUS_2               13                45
  CLUS_3               10                72
  CLUS_4                4                30
  CLUS_5                9                66
  CLUS_6                6                28
  CLUS_7                6                30
  CLUS_8               14                38
  CLUS_9                7                35
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       18     25     47
  8Q LOSS WILD-TYPE    153    181    155
D57V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              18               153
  CLUS_2              25               181
  CLUS_3              47               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
  8Q LOSS MUTATED       37     24     27
  8Q LOSS WILD-TYPE    135    151    194
D57V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              37               135
  CLUS_2              24               151
  CLUS_3              27               194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       19     36      8
  8Q LOSS WILD-TYPE    127    153     68
D57V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              19               127
  CLUS_2              36               153
  CLUS_3               8                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED       17      7     10     29
  8Q LOSS WILD-TYPE    126     47     50    125
D57V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              17               126
  CLUS_2               7                47
  CLUS_3              10                50
  CLUS_4              29               125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        8     29     13
  8Q LOSS WILD-TYPE     71     79    100
D57V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               8                71
  CLUS_2              29                79
  CLUS_3              13               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
  8Q LOSS MUTATED       19     20     11
  8Q LOSS WILD-TYPE    127     39     84
D57V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              19               127
  CLUS_2              20                39
  CLUS_3              11                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       19     24     24
  8Q LOSS WILD-TYPE    102    158    120
D57V11, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              19               102
  CLUS_2              24               158
  CLUS_3              24               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED       10     16     26     15
  8Q LOSS WILD-TYPE     95     55    139     91
D57V12, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              10                95
  CLUS_2              16                55
  CLUS_3              26               139
  CLUS_4              15                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"
D57V13, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  2
  8Q LOSS WILD-TYPE 10  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE   10    8
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                10
  CLUS_2               2                 8
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q LOSS MUTATED        1      1      0      1      1      0
  8Q LOSS WILD-TYPE      5      1      2      5      3      2
D57V14, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               1                 1
  CLUS_3               0                 2
  CLUS_4               1                 5
  CLUS_5               1                 3
  CLUS_6               0                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED      106     77     65
  9P LOSS WILD-TYPE    109    139     61
D58V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1             106               109
  CLUS_2              77               139
  CLUS_3              65                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      125     70     53
  9P LOSS WILD-TYPE    185     88     36
D58V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1             125               185
  CLUS_2              70                88
  CLUS_3              53                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       72     78     97
  9P LOSS WILD-TYPE     87     86    135
D58V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              72                87
  CLUS_2              78                86
  CLUS_3              97               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9P LOSS MUTATED       35      26     33     29     17     28     15     15
  9P LOSS WILD-TYPE     50      31     25     53     17     47     19     21
                   vv
clus                CLUS_8 CLUS_9
  9P LOSS MUTATED       30     19
  9P LOSS WILD-TYPE     22     23
D58V4, multiclass
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               35                50
  CLUS_10              26                31
  CLUS_2               33                25
  CLUS_3               29                53
  CLUS_4               17                17
  CLUS_5               28                47
  CLUS_6               15                19
  CLUS_7               15                21
  CLUS_8               30                22
  CLUS_9               19                23
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       79     78    105
  9P LOSS WILD-TYPE     92    128     97
D58V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              79                92
  CLUS_2              78               128
  CLUS_3             105                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       85     84     86
  9P LOSS WILD-TYPE     87     91    135
D58V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              85                87
  CLUS_2              84                91
  CLUS_3              86               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
  9P LOSS MUTATED       64     78     32
  9P LOSS WILD-TYPE     82    111     44
D58V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              64                82
  CLUS_2              78               111
  CLUS_3              32                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       66     23     19     66
  9P LOSS WILD-TYPE     77     31     41     88
D58V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              66                77
  CLUS_2              23                31
  CLUS_3              19                41
  CLUS_4              66                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
  9P LOSS MUTATED       27     52     54
  9P LOSS WILD-TYPE     52     56     59
D58V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              27                52
  CLUS_2              52                56
  CLUS_3              54                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       55     32     46
  9P LOSS WILD-TYPE     91     27     49
D58V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              55                91
  CLUS_2              32                27
  CLUS_3              46                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     69     72
  9P LOSS WILD-TYPE     62    113     72
D58V11, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              59                62
  CLUS_2              69               113
  CLUS_3              72                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       40     32     73     55
  9P LOSS WILD-TYPE     65     39     92     51
D58V12, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              40                65
  CLUS_2              32                39
  CLUS_3              73                92
  CLUS_4              55                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"
D58V13, binary
                   cls
clus                0 1
  9P LOSS MUTATED   8 4
  9P LOSS WILD-TYPE 4 6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8    4
  9P LOSS WILD-TYPE    4    6
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8                 4
  CLUS_2               4                 6
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P LOSS MUTATED        4      1      2      4      0      1
  9P LOSS WILD-TYPE      2      1      0      2      4      1
D58V14, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               1                 1
  CLUS_3               2                 0
  CLUS_4               4                 2
  CLUS_5               0                 4
  CLUS_6               1                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED      120     88     63
  9Q LOSS WILD-TYPE     95    128     63
D59V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1             120                95
  CLUS_2              88               128
  CLUS_3              63                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      143     72     56
  9Q LOSS WILD-TYPE    167     86     33
D59V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1             143               167
  CLUS_2              72                86
  CLUS_3              56                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       70     88    113
  9Q LOSS WILD-TYPE     89     76    119
D59V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              70                89
  CLUS_2              88                76
  CLUS_3             113               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  9Q LOSS MUTATED       31      30     34     33     21     33     21     18
  9Q LOSS WILD-TYPE     54      27     24     49     13     42     13     18
                   vv
clus                CLUS_8 CLUS_9
  9Q LOSS MUTATED       31     19
  9Q LOSS WILD-TYPE     21     23
D59V4, multiclass
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               31                54
  CLUS_10              30                27
  CLUS_2               34                24
  CLUS_3               33                49
  CLUS_4               21                13
  CLUS_5               33                42
  CLUS_6               21                13
  CLUS_7               18                18
  CLUS_8               31                21
  CLUS_9               19                23
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       81     68    137
  9Q LOSS WILD-TYPE     90    138     65
D59V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              81                90
  CLUS_2              68               138
  CLUS_3             137                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED      102     80     97
  9Q LOSS WILD-TYPE     70     95    124
D59V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1             102                70
  CLUS_2              80                95
  CLUS_3              97               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
  9Q LOSS MUTATED       70     90     32
  9Q LOSS WILD-TYPE     76     99     44
D59V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              70                76
  CLUS_2              90                99
  CLUS_3              32                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       65     30     26     71
  9Q LOSS WILD-TYPE     78     24     34     83
D59V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              65                78
  CLUS_2              30                24
  CLUS_3              26                34
  CLUS_4              71                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
  9Q LOSS MUTATED       27     62     52
  9Q LOSS WILD-TYPE     52     46     61
D59V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              27                52
  CLUS_2              62                46
  CLUS_3              52                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       57     40     44
  9Q LOSS WILD-TYPE     89     19     51
D59V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              57                89
  CLUS_2              40                19
  CLUS_3              44                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       60     80     77
  9Q LOSS WILD-TYPE     61    102     67
D59V11, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              60                61
  CLUS_2              80               102
  CLUS_3              77                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       39     39     84     55
  9Q LOSS WILD-TYPE     66     32     81     51
D59V12, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              39                66
  CLUS_2              39                32
  CLUS_3              84                81
  CLUS_4              55                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"
D59V13, binary
                   cls
clus                0 1
  9Q LOSS MUTATED   7 5
  9Q LOSS WILD-TYPE 5 5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7    5
  9Q LOSS WILD-TYPE    5    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                 5
  CLUS_2               5                 5
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q LOSS MUTATED        2      1      2      3      2      2
  9Q LOSS WILD-TYPE      4      1      0      3      2      0
D59V14, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                 4
  CLUS_2               1                 1
  CLUS_3               2                 0
  CLUS_4               3                 3
  CLUS_5               2                 2
  CLUS_6               2                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       37     41     15
  10P LOSS WILD-TYPE    178    175    111
D60V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               37                178
  CLUS_2               41                175
  CLUS_3               15                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
  10P LOSS MUTATED       53     26     14
  10P LOSS WILD-TYPE    257    132     75
D60V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               53                257
  CLUS_2               26                132
  CLUS_3               14                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       25     22     46
  10P LOSS WILD-TYPE    134    142    186
D60V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               25                134
  CLUS_2               22                142
  CLUS_3               46                186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10P LOSS MUTATED       13      11      8     13      2     14      8     11
  10P LOSS WILD-TYPE     72      46     50     69     32     61     26     25
                    vv
clus                 CLUS_8 CLUS_9
  10P LOSS MUTATED        7      6
  10P LOSS WILD-TYPE     45     36
D60V4, multiclass
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                13                 72
  CLUS_10               11                 46
  CLUS_2                 8                 50
  CLUS_3                13                 69
  CLUS_4                 2                 32
  CLUS_5                14                 61
  CLUS_6                 8                 26
  CLUS_7                11                 25
  CLUS_8                 7                 45
  CLUS_9                 6                 36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       32     31     34
  10P LOSS WILD-TYPE    139    175    168
D60V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               32                139
  CLUS_2               31                175
  CLUS_3               34                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
  10P LOSS MUTATED       36     28     32
  10P LOSS WILD-TYPE    136    147    189
D60V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               36                136
  CLUS_2               28                147
  CLUS_3               32                189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       24     34     12
  10P LOSS WILD-TYPE    122    155     64
D60V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               24                122
  CLUS_2               34                155
  CLUS_3               12                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED       25     11      9     25
  10P LOSS WILD-TYPE    118     43     51    129
D60V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               25                118
  CLUS_2               11                 43
  CLUS_3                9                 51
  CLUS_4               25                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       14     17     16
  10P LOSS WILD-TYPE     65     91     97
D60V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               14                 65
  CLUS_2               17                 91
  CLUS_3               16                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       22     11     14
  10P LOSS WILD-TYPE    124     48     81
D60V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               22                124
  CLUS_2               11                 48
  CLUS_3               14                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       15     31     27
  10P LOSS WILD-TYPE    106    151    117
D60V11, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               15                106
  CLUS_2               31                151
  CLUS_3               27                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 CLUS_4
  10P LOSS MUTATED       15     12     26     20
  10P LOSS WILD-TYPE     90     59    139     86
D60V12, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               15                 90
  CLUS_2               12                 59
  CLUS_3               26                139
  CLUS_4               20                 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"
D60V13, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    2  1
  10P LOSS WILD-TYPE 10  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    1
  10P LOSS WILD-TYPE   10    9
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P LOSS MUTATED        0      0      1      1      0      1
  10P LOSS WILD-TYPE      6      2      1      5      4      1
D60V14, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                1                  5
  CLUS_5                0                  4
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       45     48     26
  10Q LOSS WILD-TYPE    170    168    100
D61V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               45                170
  CLUS_2               48                168
  CLUS_3               26                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
  10Q LOSS MUTATED       69     31     19
  10Q LOSS WILD-TYPE    241    127     70
D61V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               69                241
  CLUS_2               31                127
  CLUS_3               19                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       32     23     64
  10Q LOSS WILD-TYPE    127    141    168
D61V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               32                127
  CLUS_2               23                141
  CLUS_3               64                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  10Q LOSS MUTATED       15      13     10     19      9     14     12     12
  10Q LOSS WILD-TYPE     70      44     48     63     25     61     22     24
                    vv
clus                 CLUS_8 CLUS_9
  10Q LOSS MUTATED        9      6
  10Q LOSS WILD-TYPE     43     36
D61V4, multiclass
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                15                 70
  CLUS_10               13                 44
  CLUS_2                10                 48
  CLUS_3                19                 63
  CLUS_4                 9                 25
  CLUS_5                14                 61
  CLUS_6                12                 22
  CLUS_7                12                 24
  CLUS_8                 9                 43
  CLUS_9                 6                 36
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       33     35     56
  10Q LOSS WILD-TYPE    138    171    146
D61V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               33                138
  CLUS_2               35                171
  CLUS_3               56                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
  10Q LOSS MUTATED       53     27     43
  10Q LOSS WILD-TYPE    119    148    178
D61V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               53                119
  CLUS_2               27                148
  CLUS_3               43                178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       29     45     15
  10Q LOSS WILD-TYPE    117    144     61
D61V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               29                117
  CLUS_2               45                144
  CLUS_3               15                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       33     14     12     30
  10Q LOSS WILD-TYPE    110     40     48    124
D61V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               33                110
  CLUS_2               14                 40
  CLUS_3               12                 48
  CLUS_4               30                124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       15     27     26
  10Q LOSS WILD-TYPE     64     81     87
D61V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               15                 64
  CLUS_2               27                 81
  CLUS_3               26                 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
  10Q LOSS MUTATED       32     15     21
  10Q LOSS WILD-TYPE    114     44     74
D61V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               32                114
  CLUS_2               15                 44
  CLUS_3               21                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       23     42     32
  10Q LOSS WILD-TYPE     98    140    112
D61V11, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               23                 98
  CLUS_2               42                140
  CLUS_3               32                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
  10Q LOSS MUTATED       20     12     43     22
  10Q LOSS WILD-TYPE     85     59    122     84
D61V12, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               20                 85
  CLUS_2               12                 59
  CLUS_3               43                122
  CLUS_4               22                 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"
D61V13, binary
                    cls
clus                 0 1
  10Q LOSS MUTATED   5 2
  10Q LOSS WILD-TYPE 7 8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    2
  10Q LOSS WILD-TYPE    7    8
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q LOSS MUTATED        3      0      1      1      1      1
  10Q LOSS WILD-TYPE      3      2      1      5      3      1
D61V14, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                1                  5
  CLUS_5                1                  3
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       82     66     41
  11P LOSS WILD-TYPE    133    150     85
D62V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               82                133
  CLUS_2               66                150
  CLUS_3               41                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       91     57     41
  11P LOSS WILD-TYPE    219    101     48
D62V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               91                219
  CLUS_2               57                101
  CLUS_3               41                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       49     55     84
  11P LOSS WILD-TYPE    110    109    148
D62V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               49                110
  CLUS_2               55                109
  CLUS_3               84                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11P LOSS MUTATED       25      20     20     24      9     20     16     15
  11P LOSS WILD-TYPE     60      37     38     58     25     55     18     21
                    vv
clus                 CLUS_8 CLUS_9
  11P LOSS MUTATED       23     16
  11P LOSS WILD-TYPE     29     26
D62V4, multiclass
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                25                 60
  CLUS_10               20                 37
  CLUS_2                20                 38
  CLUS_3                24                 58
  CLUS_4                 9                 25
  CLUS_5                20                 55
  CLUS_6                16                 18
  CLUS_7                15                 21
  CLUS_8                23                 29
  CLUS_9                16                 26
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       54     65     79
  11P LOSS WILD-TYPE    117    141    123
D62V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               54                117
  CLUS_2               65                141
  CLUS_3               79                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
  11P LOSS MUTATED       72     54     67
  11P LOSS WILD-TYPE    100    121    154
D62V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               72                100
  CLUS_2               54                121
  CLUS_3               67                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
  11P LOSS MUTATED       55     63     22
  11P LOSS WILD-TYPE     91    126     54
D62V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               55                 91
  CLUS_2               63                126
  CLUS_3               22                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED       50     20     21     49
  11P LOSS WILD-TYPE     93     34     39    105
D62V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               50                 93
  CLUS_2               20                 34
  CLUS_3               21                 39
  CLUS_4               49                105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       20     42     39
  11P LOSS WILD-TYPE     59     66     74
D62V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               20                 59
  CLUS_2               42                 66
  CLUS_3               39                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       40     24     37
  11P LOSS WILD-TYPE    106     35     58
D62V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               40                106
  CLUS_2               24                 35
  CLUS_3               37                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       43     67     44
  11P LOSS WILD-TYPE     78    115    100
D62V11, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               43                 78
  CLUS_2               67                115
  CLUS_3               44                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED       40     22     64     28
  11P LOSS WILD-TYPE     65     49    101     78
D62V12, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               40                 65
  CLUS_2               22                 49
  CLUS_3               64                101
  CLUS_4               28                 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"
D62V13, binary
                    cls
clus                 0 1
  11P LOSS MUTATED   4 1
  11P LOSS WILD-TYPE 8 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    1
  11P LOSS WILD-TYPE    8    9
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P LOSS MUTATED        1      0      1      1      1      1
  11P LOSS WILD-TYPE      5      2      1      5      3      1
D62V14, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                1                  5
  CLUS_5                1                  3
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       63     50     30
  11Q LOSS WILD-TYPE    152    166     96
D63V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               63                152
  CLUS_2               50                166
  CLUS_3               30                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       81     41     21
  11Q LOSS WILD-TYPE    229    117     68
D63V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               81                229
  CLUS_2               41                117
  CLUS_3               21                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       36     37     68
  11Q LOSS WILD-TYPE    123    127    164
D63V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               36                123
  CLUS_2               37                127
  CLUS_3               68                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  11Q LOSS MUTATED       18      20     14     18      7     19     13     10
  11Q LOSS WILD-TYPE     67      37     44     64     27     56     21     26
                    vv
clus                 CLUS_8 CLUS_9
  11Q LOSS MUTATED       13      9
  11Q LOSS WILD-TYPE     39     33
D63V4, multiclass
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                18                 67
  CLUS_10               20                 37
  CLUS_2                14                 44
  CLUS_3                18                 64
  CLUS_4                 7                 27
  CLUS_5                19                 56
  CLUS_6                13                 21
  CLUS_7                10                 26
  CLUS_8                13                 39
  CLUS_9                 9                 33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       38     43     67
  11Q LOSS WILD-TYPE    133    163    135
D63V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               38                133
  CLUS_2               43                163
  CLUS_3               67                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
  11Q LOSS MUTATED       55     41     49
  11Q LOSS WILD-TYPE    117    134    172
D63V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               55                117
  CLUS_2               41                134
  CLUS_3               49                172
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       33     54     17
  11Q LOSS WILD-TYPE    113    135     59
D63V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               33                113
  CLUS_2               54                135
  CLUS_3               17                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       38     18     13     35
  11Q LOSS WILD-TYPE    105     36     47    119
D63V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               38                105
  CLUS_2               18                 36
  CLUS_3               13                 47
  CLUS_4               35                119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       16     33     24
  11Q LOSS WILD-TYPE     63     75     89
D63V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               16                 63
  CLUS_2               33                 75
  CLUS_3               24                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       32     18     23
  11Q LOSS WILD-TYPE    114     41     72
D63V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               32                114
  CLUS_2               18                 41
  CLUS_3               23                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       33     52     33
  11Q LOSS WILD-TYPE     88    130    111
D63V11, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               33                 88
  CLUS_2               52                130
  CLUS_3               33                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 CLUS_4
  11Q LOSS MUTATED       28     19     51     20
  11Q LOSS WILD-TYPE     77     52    114     86
D63V12, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               28                 77
  CLUS_2               19                 52
  CLUS_3               51                114
  CLUS_4               20                 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"
D63V13, binary
                    cls
clus                 0 1
  11Q LOSS MUTATED   3 1
  11Q LOSS WILD-TYPE 9 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    1
  11Q LOSS WILD-TYPE    9    9
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q LOSS MUTATED        0      0      1      1      1      1
  11Q LOSS WILD-TYPE      6      2      1      5      3      1
D63V14, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                1                  5
  CLUS_5                1                  3
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       18     32     27
  12P LOSS WILD-TYPE    197    184     99
D64V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               18                197
  CLUS_2               32                184
  CLUS_3               27                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       42     30      5
  12P LOSS WILD-TYPE    268    128     84
D64V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               42                268
  CLUS_2               30                128
  CLUS_3                5                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       25     20     32
  12P LOSS WILD-TYPE    134    144    200
D64V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               25                134
  CLUS_2               20                144
  CLUS_3               32                200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12P LOSS MUTATED       12      12      6     11      4     12      1     11
  12P LOSS WILD-TYPE     73      45     52     71     30     63     33     25
                    vv
clus                 CLUS_8 CLUS_9
  12P LOSS MUTATED        1      7
  12P LOSS WILD-TYPE     51     35
D64V4, multiclass
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                12                 73
  CLUS_10               12                 45
  CLUS_2                 6                 52
  CLUS_3                11                 71
  CLUS_4                 4                 30
  CLUS_5                12                 63
  CLUS_6                 1                 33
  CLUS_7                11                 25
  CLUS_8                 1                 51
  CLUS_9                 7                 35
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     39     14
  12P LOSS WILD-TYPE    145    167    188
D64V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               26                145
  CLUS_2               39                167
  CLUS_3               14                188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       18     24     36
  12P LOSS WILD-TYPE    154    151    185
D64V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               18                154
  CLUS_2               24                151
  CLUS_3               36                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       22     23      9
  12P LOSS WILD-TYPE    124    166     67
D64V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               22                124
  CLUS_2               23                166
  CLUS_3                9                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED       21      9      8     16
  12P LOSS WILD-TYPE    122     45     52    138
D64V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               21                122
  CLUS_2                9                 45
  CLUS_3                8                 52
  CLUS_4               16                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       10     12     19
  12P LOSS WILD-TYPE     69     96     94
D64V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               10                 69
  CLUS_2               12                 96
  CLUS_3               19                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       18      5     18
  12P LOSS WILD-TYPE    128     54     77
D64V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               18                128
  CLUS_2                5                 54
  CLUS_3               18                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       18     35     11
  12P LOSS WILD-TYPE    103    147    133
D64V11, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               18                103
  CLUS_2               35                147
  CLUS_3               11                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
  12P LOSS MUTATED       24      5     26      9
  12P LOSS WILD-TYPE     81     66    139     97
D64V12, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               24                 81
  CLUS_2                5                 66
  CLUS_3               26                139
  CLUS_4                9                 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"
D64V13, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    1  3
  12P LOSS WILD-TYPE 11  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    3
  12P LOSS WILD-TYPE   11    7
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                3                  7
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P LOSS MUTATED        1      0      1      2      0      0
  12P LOSS WILD-TYPE      5      2      1      4      4      2
D64V14, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                  5
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                2                  4
  CLUS_5                0                  4
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       29     46     25
  12Q LOSS WILD-TYPE    186    170    101
D65V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               29                186
  CLUS_2               46                170
  CLUS_3               25                101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       58     33      9
  12Q LOSS WILD-TYPE    252    125     80
D65V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               58                252
  CLUS_2               33                125
  CLUS_3                9                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       28     33     40
  12Q LOSS WILD-TYPE    131    131    192
D65V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               28                131
  CLUS_2               33                131
  CLUS_3               40                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  12Q LOSS MUTATED       15      12      6     15      6     17      4     12
  12Q LOSS WILD-TYPE     70      45     52     67     28     58     30     24
                    vv
clus                 CLUS_8 CLUS_9
  12Q LOSS MUTATED        5      9
  12Q LOSS WILD-TYPE     47     33
D65V4, multiclass
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                15                 70
  CLUS_10               12                 45
  CLUS_2                 6                 52
  CLUS_3                15                 67
  CLUS_4                 6                 28
  CLUS_5                17                 58
  CLUS_6                 4                 30
  CLUS_7                12                 24
  CLUS_8                 5                 47
  CLUS_9                 9                 33
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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     49     27
  12Q LOSS WILD-TYPE    142    157    175
D65V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               29                142
  CLUS_2               49                157
  CLUS_3               27                175
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       24     35     44
  12Q LOSS WILD-TYPE    148    140    177
D65V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               24                148
  CLUS_2               35                140
  CLUS_3               44                177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       30     25     17
  12Q LOSS WILD-TYPE    116    164     59
D65V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               30                116
  CLUS_2               25                164
  CLUS_3               17                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       26     12      8     26
  12Q LOSS WILD-TYPE    117     42     52    128
D65V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               26                117
  CLUS_2               12                 42
  CLUS_3                8                 52
  CLUS_4               26                128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED        9     16     24
  12Q LOSS WILD-TYPE     70     92     89
D65V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                9                 70
  CLUS_2               16                 92
  CLUS_3               24                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       21      5     23
  12Q LOSS WILD-TYPE    125     54     72
D65V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               21                125
  CLUS_2                5                 54
  CLUS_3               23                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       24     40     16
  12Q LOSS WILD-TYPE     97    142    128
D65V11, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               24                 97
  CLUS_2               40                142
  CLUS_3               16                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 CLUS_4
  12Q LOSS MUTATED       27      9     32     12
  12Q LOSS WILD-TYPE     78     62    133     94
D65V12, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               27                 78
  CLUS_2                9                 62
  CLUS_3               32                133
  CLUS_4               12                 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"
D65V13, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1  4
  12Q LOSS WILD-TYPE 11  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    4
  12Q LOSS WILD-TYPE   11    6
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                4                  6
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q LOSS MUTATED        0      0      1      4      0      0
  12Q LOSS WILD-TYPE      6      2      1      2      4      2
D65V14, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                  6
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                4                  2
  CLUS_5                0                  4
  CLUS_6                0                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED      111    129     57
  13Q LOSS WILD-TYPE    104     87     69
D66V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1              111                104
  CLUS_2              129                 87
  CLUS_3               57                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED      182     78     37
  13Q LOSS WILD-TYPE    128     80     52
D66V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1              182                128
  CLUS_2               78                 80
  CLUS_3               37                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       85     85    128
  13Q LOSS WILD-TYPE     74     79    104
D66V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               85                 74
  CLUS_2               85                 79
  CLUS_3              128                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"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  13Q LOSS MUTATED       46      29     38     50     17     30     13     26
  13Q LOSS WILD-TYPE     39      28     20     32     17     45     21     10
                    vv
clus                 CLUS_8 CLUS_9
  13Q LOSS MUTATED       25     24
  13Q LOSS WILD-TYPE     27     18
D66V4, multiclass
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                46                 39
  CLUS_10               29                 28
  CLUS_2                38                 20
  CLUS_3                50                 32
  CLUS_4                17                 17
  CLUS_5                30                 45
  CLUS_6                13                 21
  CLUS_7                26                 10
  CLUS_8                25                 27
  CLUS_9                24                 18
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       79    121    110
  13Q LOSS WILD-TYPE     92     85     92
D66V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               79                 92
  CLUS_2              121                 85
  CLUS_3              110                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       89     72    144
  13Q LOSS WILD-TYPE     83    103     77
D66V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               89                 83
  CLUS_2               72                103
  CLUS_3              144                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       64    114     40
  13Q LOSS WILD-TYPE     82     75     36
D66V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               64                 82
  CLUS_2              114                 75
  CLUS_3               40                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED       63     30     41     84
  13Q LOSS WILD-TYPE     80     24     19     70
D66V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               63                 80
  CLUS_2               30                 24
  CLUS_3               41                 19
  CLUS_4               84                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       47     59     52
  13Q LOSS WILD-TYPE     32     49     61
D66V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               47                 32
  CLUS_2               59                 49
  CLUS_3               52                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       83     31     44
  13Q LOSS WILD-TYPE     63     28     51
D66V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               83                 63
  CLUS_2               31                 28
  CLUS_3               44                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       56    103     76
  13Q LOSS WILD-TYPE     65     79     68
D66V11, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               56                 65
  CLUS_2              103                 79
  CLUS_3               76                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED       61     35     82     57
  13Q LOSS WILD-TYPE     44     36     83     49
D66V12, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               61                 44
  CLUS_2               35                 36
  CLUS_3               82                 83
  CLUS_4               57                 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"
D66V13, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   8 5
  13Q LOSS WILD-TYPE 4 5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    5
  13Q LOSS WILD-TYPE    4    5
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                8                  4
  CLUS_2                5                  5
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q LOSS MUTATED        5      2      1      1      3      1
  13Q LOSS WILD-TYPE      1      0      1      5      1      1
D66V14, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                5                  1
  CLUS_2                2                  0
  CLUS_3                1                  1
  CLUS_4                1                  5
  CLUS_5                3                  1
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       88     74     42
  14Q LOSS WILD-TYPE    127    142     84
D67V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               88                127
  CLUS_2               74                142
  CLUS_3               42                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED      111     53     40
  14Q LOSS WILD-TYPE    199    105     49
D67V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1              111                199
  CLUS_2               53                105
  CLUS_3               40                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       57     61     86
  14Q LOSS WILD-TYPE    102    103    146
D67V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               57                102
  CLUS_2               61                103
  CLUS_3               86                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  14Q LOSS MUTATED       25      22     29     28      9     28     15     13
  14Q LOSS WILD-TYPE     60      35     29     54     25     47     19     23
                    vv
clus                 CLUS_8 CLUS_9
  14Q LOSS MUTATED       21     14
  14Q LOSS WILD-TYPE     31     28
D67V4, multiclass
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                25                 60
  CLUS_10               22                 35
  CLUS_2                29                 29
  CLUS_3                28                 54
  CLUS_4                 9                 25
  CLUS_5                28                 47
  CLUS_6                15                 19
  CLUS_7                13                 23
  CLUS_8                21                 31
  CLUS_9                14                 28
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       52     58    105
  14Q LOSS WILD-TYPE    119    148     97
D67V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               52                119
  CLUS_2               58                148
  CLUS_3              105                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       81     58     70
  14Q LOSS WILD-TYPE     91    117    151
D67V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               81                 91
  CLUS_2               58                117
  CLUS_3               70                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
  14Q LOSS MUTATED       50     70     26
  14Q LOSS WILD-TYPE     96    119     50
D67V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               50                 96
  CLUS_2               70                119
  CLUS_3               26                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED       46     20     23     57
  14Q LOSS WILD-TYPE     97     34     37     97
D67V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               46                 97
  CLUS_2               20                 34
  CLUS_3               23                 37
  CLUS_4               57                 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 LOSS MUTATED       19     49     36
  14Q LOSS WILD-TYPE     60     59     77
D67V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               19                 60
  CLUS_2               49                 59
  CLUS_3               36                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       36     34     34
  14Q LOSS WILD-TYPE    110     25     61
D67V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               36                110
  CLUS_2               34                 25
  CLUS_3               34                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       44     64     55
  14Q LOSS WILD-TYPE     77    118     89
D67V11, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               44                 77
  CLUS_2               64                118
  CLUS_3               55                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED       32     24     66     41
  14Q LOSS WILD-TYPE     73     47     99     65
D67V12, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               32                 73
  CLUS_2               24                 47
  CLUS_3               66                 99
  CLUS_4               41                 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"
D67V13, binary
                    cls
clus                 0 1
  14Q LOSS MUTATED   5 2
  14Q LOSS WILD-TYPE 7 8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5    2
  14Q LOSS WILD-TYPE    7    8
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                2                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q LOSS MUTATED        4      0      0      2      0      1
  14Q LOSS WILD-TYPE      2      2      2      4      4      1
D67V14, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                  2
  CLUS_2                0                  2
  CLUS_3                0                  2
  CLUS_4                2                  4
  CLUS_5                0                  4
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED      126     87     57
  15Q LOSS WILD-TYPE     89    129     69
D68V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1              126                 89
  CLUS_2               87                129
  CLUS_3               57                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED      150     66     54
  15Q LOSS WILD-TYPE    160     92     35
D68V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1              150                160
  CLUS_2               66                 92
  CLUS_3               54                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       62     70    138
  15Q LOSS WILD-TYPE     97     94     94
D68V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               62                 97
  CLUS_2               70                 94
  CLUS_3              138                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  15Q LOSS MUTATED       26      27     34     41     18     42     23     18
  15Q LOSS WILD-TYPE     59      30     24     41     16     33     11     18
                    vv
clus                 CLUS_8 CLUS_9
  15Q LOSS MUTATED       30     11
  15Q LOSS WILD-TYPE     22     31
D68V4, multiclass
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                26                 59
  CLUS_10               27                 30
  CLUS_2                34                 24
  CLUS_3                41                 41
  CLUS_4                18                 16
  CLUS_5                42                 33
  CLUS_6                23                 11
  CLUS_7                18                 18
  CLUS_8                30                 22
  CLUS_9                11                 31
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       65     74    141
  15Q LOSS WILD-TYPE    106    132     61
D68V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               65                106
  CLUS_2               74                132
  CLUS_3              141                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      114     69     94
  15Q LOSS WILD-TYPE     58    106    127
D68V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1              114                 58
  CLUS_2               69                106
  CLUS_3               94                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 LOSS MUTATED       63     98     42
  15Q LOSS WILD-TYPE     83     91     34
D68V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               63                 83
  CLUS_2               98                 91
  CLUS_3               42                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED       69     29     30     75
  15Q LOSS WILD-TYPE     74     25     30     79
D68V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               69                 74
  CLUS_2               29                 25
  CLUS_3               30                 30
  CLUS_4               75                 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
  15Q LOSS MUTATED       27     62     51
  15Q LOSS WILD-TYPE     52     46     62
D68V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               27                 52
  CLUS_2               62                 46
  CLUS_3               51                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       66     33     41
  15Q LOSS WILD-TYPE     80     26     54
D68V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               66                 80
  CLUS_2               33                 26
  CLUS_3               41                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED       55    108     63
  15Q LOSS WILD-TYPE     66     74     81
D68V11, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               55                 66
  CLUS_2              108                 74
  CLUS_3               63                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED       43     37    103     43
  15Q LOSS WILD-TYPE     62     34     62     63
D68V12, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               43                 62
  CLUS_2               37                 34
  CLUS_3              103                 62
  CLUS_4               43                 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"
D68V13, binary
                    cls
clus                 0 1
  15Q LOSS MUTATED   4 8
  15Q LOSS WILD-TYPE 8 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    8
  15Q LOSS WILD-TYPE    8    2
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                8                  2
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q LOSS MUTATED        3      2      0      4      2      1
  15Q LOSS WILD-TYPE      3      0      2      2      2      1
D68V14, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                2                  0
  CLUS_3                0                  2
  CLUS_4                4                  2
  CLUS_5                2                  2
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED      122    119     79
  16P LOSS WILD-TYPE     93     97     47
D69V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1              122                 93
  CLUS_2              119                 97
  CLUS_3               79                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED      178     93     49
  16P LOSS WILD-TYPE    132     65     40
D69V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1              178                132
  CLUS_2               93                 65
  CLUS_3               49                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       97     81    142
  16P LOSS WILD-TYPE     62     83     90
D69V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               97                 62
  CLUS_2               81                 83
  CLUS_3              142                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16P LOSS MUTATED       50      29     28     49     24     42     20     26
  16P LOSS WILD-TYPE     35      28     30     33     10     33     14     10
                    vv
clus                 CLUS_8 CLUS_9
  16P LOSS MUTATED       31     21
  16P LOSS WILD-TYPE     21     21
D69V4, multiclass
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                50                 35
  CLUS_10               29                 28
  CLUS_2                28                 30
  CLUS_3                49                 33
  CLUS_4                24                 10
  CLUS_5                42                 33
  CLUS_6                20                 14
  CLUS_7                26                 10
  CLUS_8                31                 21
  CLUS_9                21                 21
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       92    116    126
  16P LOSS WILD-TYPE     79     90     76
D69V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               92                 79
  CLUS_2              116                 90
  CLUS_3              126                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED      109    102    117
  16P LOSS WILD-TYPE     63     73    104
D69V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1              109                 63
  CLUS_2              102                 73
  CLUS_3              117                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       86    110     35
  16P LOSS WILD-TYPE     60     79     41
D69V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               86                 60
  CLUS_2              110                 79
  CLUS_3               35                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       78     32     34     87
  16P LOSS WILD-TYPE     65     22     26     67
D69V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               78                 65
  CLUS_2               32                 22
  CLUS_3               34                 26
  CLUS_4               87                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       41     66     75
  16P LOSS WILD-TYPE     38     42     38
D69V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               41                 38
  CLUS_2               66                 42
  CLUS_3               75                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       86     37     59
  16P LOSS WILD-TYPE     60     22     36
D69V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               86                 60
  CLUS_2               37                 22
  CLUS_3               59                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       67    120     77
  16P LOSS WILD-TYPE     54     62     67
D69V11, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               67                 54
  CLUS_2              120                 62
  CLUS_3               77                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED       65     34    107     58
  16P LOSS WILD-TYPE     40     37     58     48
D69V12, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               65                 40
  CLUS_2               34                 37
  CLUS_3              107                 58
  CLUS_4               58                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                    cls
clus                 0 1
  16P LOSS MUTATED   7 7
  16P LOSS WILD-TYPE 5 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    7
  16P LOSS WILD-TYPE    5    3
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                7                  5
  CLUS_2                7                  3
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P LOSS MUTATED        5      1      0      4      2      2
  16P LOSS WILD-TYPE      1      1      2      2      2      0
D69V14, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                5                  1
  CLUS_2                1                  1
  CLUS_3                0                  2
  CLUS_4                4                  2
  CLUS_5                2                  2
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED      151    150     94
  16Q LOSS WILD-TYPE     64     66     32
D70V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              151                 64
  CLUS_2              150                 66
  CLUS_3               94                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      220    110     65
  16Q LOSS WILD-TYPE     90     48     24
D70V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              220                 90
  CLUS_2              110                 48
  CLUS_3               65                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      117    100    178
  16Q LOSS WILD-TYPE     42     64     54
D70V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              117                 42
  CLUS_2              100                 64
  CLUS_3              178                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  16Q LOSS MUTATED       62      35     36     64     26     52     23     30
  16Q LOSS WILD-TYPE     23      22     22     18      8     23     11      6
                    vv
clus                 CLUS_8 CLUS_9
  16Q LOSS MUTATED       42     25
  16Q LOSS WILD-TYPE     10     17
D70V4, multiclass
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                62                 23
  CLUS_10               35                 22
  CLUS_2                36                 22
  CLUS_3                64                 18
  CLUS_4                26                  8
  CLUS_5                52                 23
  CLUS_6                23                 11
  CLUS_7                30                  6
  CLUS_8                42                 10
  CLUS_9                25                 17
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      112    144    157
  16Q LOSS WILD-TYPE     59     62     45
D70V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              112                 59
  CLUS_2              144                 62
  CLUS_3              157                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED      133    125    147
  16Q LOSS WILD-TYPE     39     50     74
D70V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              133                 39
  CLUS_2              125                 50
  CLUS_3              147                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED       99    138     50
  16Q LOSS WILD-TYPE     47     51     26
D70V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               99                 47
  CLUS_2              138                 51
  CLUS_3               50                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       94     41     45    107
  16Q LOSS WILD-TYPE     49     13     15     47
D70V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               94                 49
  CLUS_2               41                 13
  CLUS_3               45                 15
  CLUS_4              107                 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
  16Q LOSS MUTATED       51     80     87
  16Q LOSS WILD-TYPE     28     28     26
D70V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               51                 28
  CLUS_2               80                 28
  CLUS_3               87                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      104     45     69
  16Q LOSS WILD-TYPE     42     14     26
D70V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              104                 42
  CLUS_2               45                 14
  CLUS_3               69                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       88    142     95
  16Q LOSS WILD-TYPE     33     40     49
D70V11, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               88                 33
  CLUS_2              142                 40
  CLUS_3               95                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       81     49    126     69
  16Q LOSS WILD-TYPE     24     22     39     37
D70V12, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               81                 24
  CLUS_2               49                 22
  CLUS_3              126                 39
  CLUS_4               69                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   10  7
  16Q LOSS WILD-TYPE  2  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     10    7
  16Q LOSS WILD-TYPE    2    3
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               10                  2
  CLUS_2                7                  3
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q LOSS MUTATED        5      1      2      5      2      2
  16Q LOSS WILD-TYPE      1      1      0      1      2      0
D70V14, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                  1
  CLUS_2                1                  1
  CLUS_3                2                  0
  CLUS_4                5                  1
  CLUS_5                2                  2
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED      171    183    106
  17P LOSS WILD-TYPE     44     33     20
D71V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              171                 44
  CLUS_2              183                 33
  CLUS_3              106                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      258    134     68
  17P LOSS WILD-TYPE     52     24     21
D71V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              258                 52
  CLUS_2              134                 24
  CLUS_3               68                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      137    128    195
  17P LOSS WILD-TYPE     22     36     37
D71V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              137                 22
  CLUS_2              128                 36
  CLUS_3              195                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17P LOSS MUTATED       72      47     48     70     27     65     30     31
  17P LOSS WILD-TYPE     13      10     10     12      7     10      4      5
                    vv
clus                 CLUS_8 CLUS_9
  17P LOSS MUTATED       34     36
  17P LOSS WILD-TYPE     18      6
D71V4, multiclass
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                72                 13
  CLUS_10               47                 10
  CLUS_2                48                 10
  CLUS_3                70                 12
  CLUS_4                27                  7
  CLUS_5                65                 10
  CLUS_6                30                  4
  CLUS_7                31                  5
  CLUS_8                34                 18
  CLUS_9                36                  6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      137    173    168
  17P LOSS WILD-TYPE     34     33     34
D71V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              137                 34
  CLUS_2              173                 33
  CLUS_3              168                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED      135    147    187
  17P LOSS WILD-TYPE     37     28     34
D71V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              135                 37
  CLUS_2              147                 28
  CLUS_3              187                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED      116    154     65
  17P LOSS WILD-TYPE     30     35     11
D71V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              116                 30
  CLUS_2              154                 35
  CLUS_3               65                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      116     47     46    126
  17P LOSS WILD-TYPE     27      7     14     28
D71V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              116                 27
  CLUS_2               47                  7
  CLUS_3               46                 14
  CLUS_4              126                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED       70     85     97
  17P LOSS WILD-TYPE      9     23     16
D71V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               70                  9
  CLUS_2               85                 23
  CLUS_3               97                 16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      125     45     82
  17P LOSS WILD-TYPE     21     14     13
D71V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              125                 21
  CLUS_2               45                 14
  CLUS_3               82                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      102    158    118
  17P LOSS WILD-TYPE     19     24     26
D71V11, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              102                 19
  CLUS_2              158                 24
  CLUS_3              118                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       92     58    142     86
  17P LOSS WILD-TYPE     13     13     23     20
D71V12, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               92                 13
  CLUS_2               58                 13
  CLUS_3              142                 23
  CLUS_4               86                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   11  9
  17P LOSS WILD-TYPE  1  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     11    9
  17P LOSS WILD-TYPE    1    1
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                  1
  CLUS_2                9                  1
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P LOSS MUTATED        6      2      2      5      3      2
  17P LOSS WILD-TYPE      0      0      0      1      1      0
D71V14, multiclass
[1] "Remove cluster labels:" "17P LOSS WILD-TYPE"    
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                20                  2 
      TCGA-04-1652       TCGA-09-2050       TCGA-09-2054       TCGA-13-0908 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-23-2077       TCGA-24-1928       TCGA-24-2036       TCGA-24-2288 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-24-2290       TCGA-24-2297       TCGA-25-2392       TCGA-25-2399 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-25-2400       TCGA-25-2404       TCGA-59-2363       TCGA-61-1918 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 
      TCGA-61-2088       TCGA-61-2098       TCGA-61-2109       TCGA-61-2111 
"17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" "17P LOSS MUTATED" 

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED      148    148     73
  17Q LOSS WILD-TYPE     67     68     53
D72V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1              148                 67
  CLUS_2              148                 68
  CLUS_3               73                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED      220     94     55
  17Q LOSS WILD-TYPE     90     64     34
D72V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1              220                 90
  CLUS_2               94                 64
  CLUS_3               55                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED      104     96    168
  17Q LOSS WILD-TYPE     55     68     64
D72V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1              104                 55
  CLUS_2               96                 68
  CLUS_3              168                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  17Q LOSS MUTATED       50      37     43     59     19     50     30     26
  17Q LOSS WILD-TYPE     35      20     15     23     15     25      4     10
                    vv
clus                 CLUS_8 CLUS_9
  17Q LOSS MUTATED       26     28
  17Q LOSS WILD-TYPE     26     14
D72V4, multiclass
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                50                 35
  CLUS_10               37                 20
  CLUS_2                43                 15
  CLUS_3                59                 23
  CLUS_4                19                 15
  CLUS_5                50                 25
  CLUS_6                30                  4
  CLUS_7                26                 10
  CLUS_8                26                 26
  CLUS_9                28                 14
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      113    138    132
  17Q LOSS WILD-TYPE     58     68     70
D72V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1              113                 58
  CLUS_2              138                 68
  CLUS_3              132                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED      110    114    152
  17Q LOSS WILD-TYPE     62     61     69
D72V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1              110                 62
  CLUS_2              114                 61
  CLUS_3              152                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED       96    121     53
  17Q LOSS WILD-TYPE     50     68     23
D72V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               96                 50
  CLUS_2              121                 68
  CLUS_3               53                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       88     35     37    110
  17Q LOSS WILD-TYPE     55     19     23     44
D72V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               88                 55
  CLUS_2               35                 19
  CLUS_3               37                 23
  CLUS_4              110                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       61     70     67
  17Q LOSS WILD-TYPE     18     38     46
D72V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               61                 18
  CLUS_2               70                 38
  CLUS_3               67                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      104     38     56
  17Q LOSS WILD-TYPE     42     21     39
D72V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1              104                 42
  CLUS_2               38                 21
  CLUS_3               56                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       72    131     96
  17Q LOSS WILD-TYPE     49     51     48
D72V11, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               72                 49
  CLUS_2              131                 51
  CLUS_3               96                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED       66     50    113     70
  17Q LOSS WILD-TYPE     39     21     52     36
D72V12, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               66                 39
  CLUS_2               50                 21
  CLUS_3              113                 52
  CLUS_4               70                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10  7
  17Q LOSS WILD-TYPE  2  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    7
  17Q LOSS WILD-TYPE    2    3
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               10                  2
  CLUS_2                7                  3
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q LOSS MUTATED        6      2      2      3      3      1
  17Q LOSS WILD-TYPE      0      0      0      3      1      1
D72V14, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                6                  0
  CLUS_2                2                  0
  CLUS_3                2                  0
  CLUS_4                3                  3
  CLUS_5                3                  1
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       86     84     58
  18P LOSS WILD-TYPE    129    132     68
D73V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               86                129
  CLUS_2               84                132
  CLUS_3               58                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED      125     66     37
  18P LOSS WILD-TYPE    185     92     52
D73V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1              125                185
  CLUS_2               66                 92
  CLUS_3               37                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       72     64     93
  18P LOSS WILD-TYPE     87    100    139
D73V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               72                 87
  CLUS_2               64                100
  CLUS_3               93                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18P LOSS MUTATED       37      16     20     27     21     40     12     17
  18P LOSS WILD-TYPE     48      41     38     55     13     35     22     19
                    vv
clus                 CLUS_8 CLUS_9
  18P LOSS MUTATED       20     19
  18P LOSS WILD-TYPE     32     23
D73V4, multiclass
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                37                 48
  CLUS_10               16                 41
  CLUS_2                20                 38
  CLUS_3                27                 55
  CLUS_4                21                 13
  CLUS_5                40                 35
  CLUS_6                12                 22
  CLUS_7                17                 19
  CLUS_8                20                 32
  CLUS_9                19                 23
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       75     79     81
  18P LOSS WILD-TYPE     96    127    121
D73V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               75                 96
  CLUS_2               79                127
  CLUS_3               81                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       59     90     83
  18P LOSS WILD-TYPE    113     85    138
D73V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               59                113
  CLUS_2               90                 85
  CLUS_3               83                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       63     71     36
  18P LOSS WILD-TYPE     83    118     40
D73V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               63                 83
  CLUS_2               71                118
  CLUS_3               36                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       56     23     30     61
  18P LOSS WILD-TYPE     87     31     30     93
D73V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               56                 87
  CLUS_2               23                 31
  CLUS_3               30                 30
  CLUS_4               61                 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
  18P LOSS MUTATED       29     48     47
  18P LOSS WILD-TYPE     50     60     66
D73V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               29                 50
  CLUS_2               48                 60
  CLUS_3               47                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       50     28     46
  18P LOSS WILD-TYPE     96     31     49
D73V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               50                 96
  CLUS_2               28                 31
  CLUS_3               46                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       53     76     58
  18P LOSS WILD-TYPE     68    106     86
D73V11, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               53                 68
  CLUS_2               76                106
  CLUS_3               58                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED       47     30     72     38
  18P LOSS WILD-TYPE     58     41     93     68
D73V12, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               47                 58
  CLUS_2               30                 41
  CLUS_3               72                 93
  CLUS_4               38                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                    cls
clus                 0 1
  18P LOSS MUTATED   4 5
  18P LOSS WILD-TYPE 8 5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    5
  18P LOSS WILD-TYPE    8    5
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                5                  5
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P LOSS MUTATED        3      1      0      2      1      2
  18P LOSS WILD-TYPE      3      1      2      4      3      0
D73V14, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                1                  1
  CLUS_3                0                  2
  CLUS_4                2                  4
  CLUS_5                1                  3
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED      115    101     66
  18Q LOSS WILD-TYPE    100    115     60
D74V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1              115                100
  CLUS_2              101                115
  CLUS_3               66                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      157     79     46
  18Q LOSS WILD-TYPE    153     79     43
D74V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1              157                153
  CLUS_2               79                 79
  CLUS_3               46                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       89     78    116
  18Q LOSS WILD-TYPE     70     86    116
D74V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               89                 70
  CLUS_2               78                 86
  CLUS_3              116                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  18Q LOSS MUTATED       44      28     26     40     21     40     18     17
  18Q LOSS WILD-TYPE     41      29     32     42     13     35     16     19
                    vv
clus                 CLUS_8 CLUS_9
  18Q LOSS MUTATED       27     22
  18Q LOSS WILD-TYPE     25     20
D74V4, multiclass
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                44                 41
  CLUS_10               28                 29
  CLUS_2                26                 32
  CLUS_3                40                 42
  CLUS_4                21                 13
  CLUS_5                40                 35
  CLUS_6                18                 16
  CLUS_7                17                 19
  CLUS_8                27                 25
  CLUS_9                22                 20
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       88    106     99
  18Q LOSS WILD-TYPE     83    100    103
D74V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               88                 83
  CLUS_2              106                100
  CLUS_3               99                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
  18Q LOSS MUTATED       82    101    107
  18Q LOSS WILD-TYPE     90     74    114
D74V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               82                 90
  CLUS_2              101                 74
  CLUS_3              107                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
  18Q LOSS MUTATED       74     92     38
  18Q LOSS WILD-TYPE     72     97     38
D74V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               74                 72
  CLUS_2               92                 97
  CLUS_3               38                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       71     27     36     70
  18Q LOSS WILD-TYPE     72     27     24     84
D74V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               71                 72
  CLUS_2               27                 27
  CLUS_3               36                 24
  CLUS_4               70                 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
  18Q LOSS MUTATED       36     62     55
  18Q LOSS WILD-TYPE     43     46     58
D74V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               36                 43
  CLUS_2               62                 46
  CLUS_3               55                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       64     37     52
  18Q LOSS WILD-TYPE     82     22     43
D74V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               64                 82
  CLUS_2               37                 22
  CLUS_3               52                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       64     94     74
  18Q LOSS WILD-TYPE     57     88     70
D74V11, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               64                 57
  CLUS_2               94                 88
  CLUS_3               74                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED       57     39     85     51
  18Q LOSS WILD-TYPE     48     32     80     55
D74V12, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               57                 48
  CLUS_2               39                 32
  CLUS_3               85                 80
  CLUS_4               51                 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"
D74V13, binary
                    cls
clus                 0 1
  18Q LOSS MUTATED   5 6
  18Q LOSS WILD-TYPE 7 4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    6
  18Q LOSS WILD-TYPE    7    4
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                6                  4
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q LOSS MUTATED        3      2      1      1      2      2
  18Q LOSS WILD-TYPE      3      0      1      5      2      0
D74V14, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                2                  0
  CLUS_3                1                  1
  CLUS_4                1                  5
  CLUS_5                2                  2
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       69     68     41
  19P LOSS WILD-TYPE    146    148     85
D75V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               69                146
  CLUS_2               68                148
  CLUS_3               41                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      101     45     32
  19P LOSS WILD-TYPE    209    113     57
D75V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1              101                209
  CLUS_2               45                113
  CLUS_3               32                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       45     51     82
  19P LOSS WILD-TYPE    114    113    150
D75V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               45                114
  CLUS_2               51                113
  CLUS_3               82                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19P LOSS MUTATED       26      16     20     31      8     20     18      9
  19P LOSS WILD-TYPE     59      41     38     51     26     55     16     27
                    vv
clus                 CLUS_8 CLUS_9
  19P LOSS MUTATED       11     19
  19P LOSS WILD-TYPE     41     23
D75V4, multiclass
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                26                 59
  CLUS_10               16                 41
  CLUS_2                20                 38
  CLUS_3                31                 51
  CLUS_4                 8                 26
  CLUS_5                20                 55
  CLUS_6                18                 16
  CLUS_7                 9                 27
  CLUS_8                11                 41
  CLUS_9                19                 23
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       56     50     79
  19P LOSS WILD-TYPE    115    156    123
D75V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               56                115
  CLUS_2               50                156
  CLUS_3               79                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
  19P LOSS MUTATED       69     49     62
  19P LOSS WILD-TYPE    103    126    159
D75V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               69                103
  CLUS_2               49                126
  CLUS_3               62                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
  19P LOSS MUTATED       36     54     33
  19P LOSS WILD-TYPE    110    135     43
D75V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               36                110
  CLUS_2               54                135
  CLUS_3               33                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED       36     24     20     43
  19P LOSS WILD-TYPE    107     30     40    111
D75V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               36                107
  CLUS_2               24                 30
  CLUS_3               20                 40
  CLUS_4               43                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       24     35     40
  19P LOSS WILD-TYPE     55     73     73
D75V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               24                 55
  CLUS_2               35                 73
  CLUS_3               40                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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     25     29
  19P LOSS WILD-TYPE    101     34     66
D75V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               45                101
  CLUS_2               25                 34
  CLUS_3               29                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       41     56     51
  19P LOSS WILD-TYPE     80    126     93
D75V11, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               41                 80
  CLUS_2               56                126
  CLUS_3               51                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED       26     26     63     33
  19P LOSS WILD-TYPE     79     45    102     73
D75V12, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               26                 79
  CLUS_2               26                 45
  CLUS_3               63                102
  CLUS_4               33                 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"
D75V13, binary
                    cls
clus                 0 1
  19P LOSS MUTATED   8 1
  19P LOSS WILD-TYPE 4 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    1
  19P LOSS WILD-TYPE    4    9
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                8                  4
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P LOSS MUTATED        3      0      2      1      1      2
  19P LOSS WILD-TYPE      3      2      0      5      3      0
D75V14, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                  3
  CLUS_2                0                  2
  CLUS_3                2                  0
  CLUS_4                1                  5
  CLUS_5                1                  3
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       70     64     36
  19Q LOSS WILD-TYPE    145    152     90
D76V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               70                145
  CLUS_2               64                152
  CLUS_3               36                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED      101     40     29
  19Q LOSS WILD-TYPE    209    118     60
D76V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1              101                209
  CLUS_2               40                118
  CLUS_3               29                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       48     43     79
  19Q LOSS WILD-TYPE    111    121    153
D76V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               48                111
  CLUS_2               43                121
  CLUS_3               79                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  19Q LOSS MUTATED       29      16     16     31      7     18     18      9
  19Q LOSS WILD-TYPE     56      41     42     51     27     57     16     27
                    vv
clus                 CLUS_8 CLUS_9
  19Q LOSS MUTATED        9     17
  19Q LOSS WILD-TYPE     43     25
D76V4, multiclass
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                29                 56
  CLUS_10               16                 41
  CLUS_2                16                 42
  CLUS_3                31                 51
  CLUS_4                 7                 27
  CLUS_5                18                 57
  CLUS_6                18                 16
  CLUS_7                 9                 27
  CLUS_8                 9                 43
  CLUS_9                17                 25
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       61     46     71
  19Q LOSS WILD-TYPE    110    160    131
D76V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               61                110
  CLUS_2               46                160
  CLUS_3               71                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
  19Q LOSS MUTATED       64     47     62
  19Q LOSS WILD-TYPE    108    128    159
D76V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               64                108
  CLUS_2               47                128
  CLUS_3               62                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
  19Q LOSS MUTATED       34     49     31
  19Q LOSS WILD-TYPE    112    140     45
D76V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               34                112
  CLUS_2               49                140
  CLUS_3               31                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       36     21     18     39
  19Q LOSS WILD-TYPE    107     33     42    115
D76V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               36                107
  CLUS_2               21                 33
  CLUS_3               18                 42
  CLUS_4               39                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       22     31     37
  19Q LOSS WILD-TYPE     57     77     76
D76V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               22                 57
  CLUS_2               31                 77
  CLUS_3               37                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       41     22     27
  19Q LOSS WILD-TYPE    105     37     68
D76V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               41                105
  CLUS_2               22                 37
  CLUS_3               27                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       37     50     51
  19Q LOSS WILD-TYPE     84    132     93
D76V11, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               37                 84
  CLUS_2               50                132
  CLUS_3               51                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       22     24     60     32
  19Q LOSS WILD-TYPE     83     47    105     74
D76V12, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               22                 83
  CLUS_2               24                 47
  CLUS_3               60                105
  CLUS_4               32                 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"
D76V13, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    7  0
  19Q LOSS WILD-TYPE  5 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7    0
  19Q LOSS WILD-TYPE    5   10
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                7                  5
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q LOSS MUTATED        2      0      2      1      1      1
  19Q LOSS WILD-TYPE      4      2      0      5      3      1
D76V14, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                0                  2
  CLUS_3                2                  0
  CLUS_4                1                  5
  CLUS_5                1                  3
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED       15     23      9
  20P LOSS WILD-TYPE    200    193    117
D77V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               15                200
  CLUS_2               23                193
  CLUS_3                9                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
  20P LOSS MUTATED       29     12      6
  20P LOSS WILD-TYPE    281    146     83
D77V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               29                281
  CLUS_2               12                146
  CLUS_3                6                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED       14      9     24
  20P LOSS WILD-TYPE    145    155    208
D77V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               14                145
  CLUS_2                9                155
  CLUS_3               24                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20P LOSS MUTATED        8       5      3     10      2      4      1      2
  20P LOSS WILD-TYPE     77      52     55     72     32     71     33     34
                    vv
clus                 CLUS_8 CLUS_9
  20P LOSS MUTATED        7      5
  20P LOSS WILD-TYPE     45     37
D77V4, multiclass
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                 8                 77
  CLUS_10                5                 52
  CLUS_2                 3                 55
  CLUS_3                10                 72
  CLUS_4                 2                 32
  CLUS_5                 4                 71
  CLUS_6                 1                 33
  CLUS_7                 2                 34
  CLUS_8                 7                 45
  CLUS_9                 5                 37
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       17     22     11
  20P LOSS WILD-TYPE    154    184    191
D77V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               17                154
  CLUS_2               22                184
  CLUS_3               11                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED       11     17     21
  20P LOSS WILD-TYPE    161    158    200
D77V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               11                161
  CLUS_2               17                158
  CLUS_3               21                200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        6     19      5
  20P LOSS WILD-TYPE    140    170     71
D77V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                140
  CLUS_2               19                170
  CLUS_3                5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      3      5     16
  20P LOSS WILD-TYPE    137     51     55    138
D77V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                6                137
  CLUS_2                3                 51
  CLUS_3                5                 55
  CLUS_4               16                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        4      8     13
  20P LOSS WILD-TYPE     75    100    100
D77V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 75
  CLUS_2                8                100
  CLUS_3               13                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
  20P LOSS MUTATED        9      7      9
  20P LOSS WILD-TYPE    137     52     86
D77V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                9                137
  CLUS_2                7                 52
  CLUS_3                9                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        2     23     15
  20P LOSS WILD-TYPE    119    159    129
D77V11, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                119
  CLUS_2               23                159
  CLUS_3               15                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
  20P LOSS MUTATED       13      8     10      9
  20P LOSS WILD-TYPE     92     63    155     97
D77V12, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               13                 92
  CLUS_2                8                 63
  CLUS_3               10                155
  CLUS_4                9                 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"
D77V13, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    2  0
  20P LOSS WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    0
  20P LOSS WILD-TYPE   10   10
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P LOSS MUTATED        1      0      0      0      0      1
  20P LOSS WILD-TYPE      5      2      2      6      4      1
D77V14, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 20 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2399 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-25-2400         TCGA-25-2404         TCGA-57-1994 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-59-2363         TCGA-61-1918         TCGA-61-2098 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-61-2109         TCGA-61-2111 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        9     17      4
  20Q LOSS WILD-TYPE    206    199    122
D78V1, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                9                206
  CLUS_2               17                199
  CLUS_3                4                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
  20Q LOSS MUTATED       20      7      3
  20Q LOSS WILD-TYPE    290    151     86
D78V2, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1               20                290
  CLUS_2                7                151
  CLUS_3                3                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED       11      3     16
  20Q LOSS WILD-TYPE    148    161    216
D78V3, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1               11                148
  CLUS_2                3                161
  CLUS_3               16                216
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  20Q LOSS MUTATED        7       4      1      8      0      4      1      1
  20Q LOSS WILD-TYPE     78      53     57     74     34     71     33     35
                    vv
clus                 CLUS_8 CLUS_9
  20Q LOSS MUTATED        2      2
  20Q LOSS WILD-TYPE     50     40
D78V4, multiclass
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                 7                 78
  CLUS_10                4                 53
  CLUS_2                 1                 57
  CLUS_3                 8                 74
  CLUS_4                 0                 34
  CLUS_5                 4                 71
  CLUS_6                 1                 33
  CLUS_7                 1                 35
  CLUS_8                 2                 50
  CLUS_9                 2                 40
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       12     12      8
  20Q LOSS WILD-TYPE    159    194    194
D78V5, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1               12                159
  CLUS_2               12                194
  CLUS_3                8                194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        7     10     14
  20Q LOSS WILD-TYPE    165    165    207
D78V6, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                7                165
  CLUS_2               10                165
  CLUS_3               14                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        4     15      2
  20Q LOSS WILD-TYPE    142    174     74
D78V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                142
  CLUS_2               15                174
  CLUS_3                2                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        4      4      2     11
  20Q LOSS WILD-TYPE    139     50     58    143
D78V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                139
  CLUS_2                4                 50
  CLUS_3                2                 58
  CLUS_4               11                143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        2      4      9
  20Q LOSS WILD-TYPE     77    104    104
D78V9, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 77
  CLUS_2                4                104
  CLUS_3                9                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"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        5      4      6
  20Q LOSS WILD-TYPE    141     55     89
D78V10, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                5                141
  CLUS_2                4                 55
  CLUS_3                6                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        4     16      7
  20Q LOSS WILD-TYPE    117    166    137
D78V11, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                117
  CLUS_2               16                166
  CLUS_3                7                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
  20Q LOSS MUTATED       10      4      9      4
  20Q LOSS WILD-TYPE     95     67    156    102
D78V12, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1               10                 95
  CLUS_2                4                 67
  CLUS_3                9                156
  CLUS_4                4                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  0
  20Q LOSS WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    0
  20Q LOSS WILD-TYPE   10   10
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                0                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q LOSS MUTATED        1      0      0      0      0      1
  20Q LOSS WILD-TYPE      5      2      2      6      4      1
D78V14, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-04-1652         TCGA-09-2050         TCGA-09-2054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-13-0908         TCGA-23-2077         TCGA-24-1928 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-24-2036         TCGA-24-2288         TCGA-24-2289 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-24-2290         TCGA-24-2297         TCGA-25-2399 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-25-2400         TCGA-25-2404         TCGA-57-1994 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-59-2363         TCGA-61-1918         TCGA-61-2098 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-61-2109         TCGA-61-2111 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       77     73     41
  21Q LOSS WILD-TYPE    138    143     85
D79V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               77                138
  CLUS_2               73                143
  CLUS_3               41                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      104     47     40
  21Q LOSS WILD-TYPE    206    111     49
D79V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1              104                206
  CLUS_2               47                111
  CLUS_3               40                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       48     61     82
  21Q LOSS WILD-TYPE    111    103    150
D79V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               48                111
  CLUS_2               61                103
  CLUS_3               82                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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  21Q LOSS MUTATED       27      19     16     26      6     28     15     16
  21Q LOSS WILD-TYPE     58      38     42     56     28     47     19     20
                    vv
clus                 CLUS_8 CLUS_9
  21Q LOSS MUTATED       24     14
  21Q LOSS WILD-TYPE     28     28
D79V4, multiclass
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                27                 58
  CLUS_10               19                 38
  CLUS_2                16                 42
  CLUS_3                26                 56
  CLUS_4                 6                 28
  CLUS_5                28                 47
  CLUS_6                15                 19
  CLUS_7                16                 20
  CLUS_8                24                 28
  CLUS_9                14                 28
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       56     67     76
  21Q LOSS WILD-TYPE    115    139    126
D79V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               56                115
  CLUS_2               67                139
  CLUS_3               76                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
  21Q LOSS MUTATED       69     54     71
  21Q LOSS WILD-TYPE    103    121    150
D79V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               69                103
  CLUS_2               54                121
  CLUS_3               71                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
  21Q LOSS MUTATED       46     58     28
  21Q LOSS WILD-TYPE    100    131     48
D79V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               46                100
  CLUS_2               58                131
  CLUS_3               28                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED       48     18     16     50
  21Q LOSS WILD-TYPE     95     36     44    104
D79V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               48                 95
  CLUS_2               18                 36
  CLUS_3               16                 44
  CLUS_4               50                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       23     37     37
  21Q LOSS WILD-TYPE     56     71     76
D79V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               23                 56
  CLUS_2               37                 71
  CLUS_3               37                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       45     23     29
  21Q LOSS WILD-TYPE    101     36     66
D79V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               45                101
  CLUS_2               23                 36
  CLUS_3               29                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       38     66     49
  21Q LOSS WILD-TYPE     83    116     95
D79V11, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               38                 83
  CLUS_2               66                116
  CLUS_3               49                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED       32     23     61     37
  21Q LOSS WILD-TYPE     73     48    104     69
D79V12, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               32                 73
  CLUS_2               23                 48
  CLUS_3               61                104
  CLUS_4               37                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                    cls
clus                 0 1
  21Q LOSS MUTATED   5 1
  21Q LOSS WILD-TYPE 7 9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    1
  21Q LOSS WILD-TYPE    7    9
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                1                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q LOSS MUTATED        2      0      1      2      0      1
  21Q LOSS WILD-TYPE      4      2      1      4      4      1
D79V14, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  4
  CLUS_2                0                  2
  CLUS_3                1                  1
  CLUS_4                2                  4
  CLUS_5                0                  4
  CLUS_6                1                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED      175    144     93
  22Q LOSS WILD-TYPE     40     72     33
D80V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              175                 40
  CLUS_2              144                 72
  CLUS_3               93                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      224    114     74
  22Q LOSS WILD-TYPE     86     44     15
D80V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              224                 86
  CLUS_2              114                 44
  CLUS_3               74                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      110    117    185
  22Q LOSS WILD-TYPE     49     47     47
D80V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              110                 49
  CLUS_2              117                 47
  CLUS_3              185                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  22Q LOSS MUTATED       56      40     43     61     25     53     30     27
  22Q LOSS WILD-TYPE     29      17     15     21      9     22      4      9
                    vv
clus                 CLUS_8 CLUS_9
  22Q LOSS MUTATED       46     31
  22Q LOSS WILD-TYPE      6     11
D80V4, multiclass
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                56                 29
  CLUS_10               40                 17
  CLUS_2                43                 15
  CLUS_3                61                 21
  CLUS_4                25                  9
  CLUS_5                53                 22
  CLUS_6                30                  4
  CLUS_7                27                  9
  CLUS_8                46                  6
  CLUS_9                31                 11
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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      120    139    171
  22Q LOSS WILD-TYPE     51     67     31
D80V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              120                 51
  CLUS_2              139                 67
  CLUS_3              171                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      140    134    146
  22Q LOSS WILD-TYPE     32     41     75
D80V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              140                 32
  CLUS_2              134                 41
  CLUS_3              146                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED      105    151     48
  22Q LOSS WILD-TYPE     41     38     28
D80V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              105                 41
  CLUS_2              151                 38
  CLUS_3               48                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       97     37     46    124
  22Q LOSS WILD-TYPE     46     17     14     30
D80V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               97                 46
  CLUS_2               37                 17
  CLUS_3               46                 14
  CLUS_4              124                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       52     88     83
  22Q LOSS WILD-TYPE     27     20     30
D80V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               52                 27
  CLUS_2               88                 20
  CLUS_3               83                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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      101     52     70
  22Q LOSS WILD-TYPE     45      7     25
D80V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1              101                 45
  CLUS_2               52                  7
  CLUS_3               70                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       83    148    110
  22Q LOSS WILD-TYPE     38     34     34
D80V11, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               83                 38
  CLUS_2              148                 34
  CLUS_3              110                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED       78     55    131     77
  22Q LOSS WILD-TYPE     27     16     34     29
D80V12, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               78                 27
  CLUS_2               55                 16
  CLUS_3              131                 34
  CLUS_4               77                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   11  6
  22Q LOSS WILD-TYPE  1  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     11    6
  22Q LOSS WILD-TYPE    1    4
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                  1
  CLUS_2                6                  4
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q LOSS MUTATED        6      2      2      4      1      2
  22Q LOSS WILD-TYPE      0      0      0      2      3      0
D80V14, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                  0
  CLUS_2                2                  0
  CLUS_3                2                  0
  CLUS_4                4                  2
  CLUS_5                1                  3
  CLUS_6                2                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED      124    127     61
  XP LOSS WILD-TYPE     91     89     65
D81V1, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1             124                91
  CLUS_2             127                89
  CLUS_3              61                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED      183     81     48
  XP LOSS WILD-TYPE    127     77     41
D81V2, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1             183               127
  CLUS_2              81                77
  CLUS_3              48                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       80     97    135
  XP LOSS WILD-TYPE     79     67     97
D81V3, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              80                79
  CLUS_2              97                67
  CLUS_3             135                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XP LOSS MUTATED       44      34     32     47     17     46     18     20
  XP LOSS WILD-TYPE     41      23     26     35     17     29     16     16
                   vv
clus                CLUS_8 CLUS_9
  XP LOSS MUTATED       25     29
  XP LOSS WILD-TYPE     27     13
D81V4, multiclass
         clus
vv        XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               44                41
  CLUS_10              34                23
  CLUS_2               32                26
  CLUS_3               47                35
  CLUS_4               17                17
  CLUS_5               46                29
  CLUS_6               18                16
  CLUS_7               20                16
  CLUS_8               25                27
  CLUS_9               29                13
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       97    131     97
  XP LOSS WILD-TYPE     74     75    105
D81V5, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              97                74
  CLUS_2             131                75
  CLUS_3              97               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       84    101    136
  XP LOSS WILD-TYPE     88     74     85
D81V6, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              84                88
  CLUS_2             101                74
  CLUS_3             136                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       76    111     42
  XP LOSS WILD-TYPE     70     78     34
D81V7, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              76                70
  CLUS_2             111                78
  CLUS_3              42                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       65     33     39     92
  XP LOSS WILD-TYPE     78     21     21     62
D81V8, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              65                78
  CLUS_2              33                21
  CLUS_3              39                21
  CLUS_4              92                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
  XP LOSS MUTATED       47     60     61
  XP LOSS WILD-TYPE     32     48     52
D81V9, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              47                32
  CLUS_2              60                48
  CLUS_3              61                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XP LOSS MUTATED       81     34     53
  XP LOSS WILD-TYPE     65     25     42
D81V10, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              81                65
  CLUS_2              34                25
  CLUS_3              53                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       65    103     92
  XP LOSS WILD-TYPE     56     79     52
D81V11, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              65                56
  CLUS_2             103                79
  CLUS_3              92                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XP LOSS MUTATED       65     42     88     65
  XP LOSS WILD-TYPE     40     29     77     41
D81V12, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              65                40
  CLUS_2              42                29
  CLUS_3              88                77
  CLUS_4              65                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   10  8
  XP LOSS WILD-TYPE  2  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     10    8
  XP LOSS WILD-TYPE    2    2
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1              10                 2
  CLUS_2               8                 2
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XP LOSS MUTATED        4      2      2      6      2      2
  XP LOSS WILD-TYPE      2      0      0      0      2      0
D81V14, multiclass
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  CLUS_1               4                 2
  CLUS_2               2                 0
  CLUS_3               2                 0
  CLUS_4               6                 0
  CLUS_5               2                 2
  CLUS_6               2                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED      107    110     52
  XQ LOSS WILD-TYPE    108    106     74
D82V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1             107               108
  CLUS_2             110               106
  CLUS_3              52                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED      158     70     41
  XQ LOSS WILD-TYPE    152     88     48
D82V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1             158               152
  CLUS_2              70                88
  CLUS_3              41                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       72     77    120
  XQ LOSS WILD-TYPE     87     87    112
D82V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              72                87
  CLUS_2              77                87
  CLUS_3             120               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_10 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  XQ LOSS MUTATED       39      29     29     41     15     37     15     18
  XQ LOSS WILD-TYPE     46      28     29     41     19     38     19     18
                   vv
clus                CLUS_8 CLUS_9
  XQ LOSS MUTATED       22     24
  XQ LOSS WILD-TYPE     30     18
D82V4, multiclass
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               39                46
  CLUS_10              29                28
  CLUS_2               29                29
  CLUS_3               41                41
  CLUS_4               15                19
  CLUS_5               37                38
  CLUS_6               15                19
  CLUS_7               18                18
  CLUS_8               22                30
  CLUS_9               24                18
[1] 10  2
[1] TRUE
[1] "dimension of contingency table 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       92    114     74
  XQ LOSS WILD-TYPE     79     92    128
D82V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              92                79
  CLUS_2             114                92
  CLUS_3              74               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
  XQ LOSS MUTATED       73     87    117
  XQ LOSS WILD-TYPE     99     88    104
D82V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              73                99
  CLUS_2              87                88
  CLUS_3             117               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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       62     91     39
  XQ LOSS WILD-TYPE     84     98     37
D82V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              62                84
  CLUS_2              91                98
  CLUS_3              39                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       56     30     33     73
  XQ LOSS WILD-TYPE     87     24     27     81
D82V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              56                87
  CLUS_2              30                24
  CLUS_3              33                27
  CLUS_4              73                81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       41     52     51
  XQ LOSS WILD-TYPE     38     56     62
D82V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              41                38
  CLUS_2              52                56
  CLUS_3              51                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       73     29     42
  XQ LOSS WILD-TYPE     73     30     53
D82V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              73                73
  CLUS_2              29                30
  CLUS_3              42                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       56     90     75
  XQ LOSS WILD-TYPE     65     92     69
D82V11, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              56                65
  CLUS_2              90                92
  CLUS_3              75                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED       57     34     77     53
  XQ LOSS WILD-TYPE     48     37     88     53
D82V12, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              57                48
  CLUS_2              34                37
  CLUS_3              77                88
  CLUS_4              53                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"
D82V13, binary
                   cls
clus                0 1
  XQ LOSS MUTATED   8 7
  XQ LOSS WILD-TYPE 4 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8    7
  XQ LOSS WILD-TYPE    4    3
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               8                 4
  CLUS_2               7                 3
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ LOSS MUTATED        2      2      2      5      2      2
  XQ LOSS WILD-TYPE      4      0      0      1      2      0
D82V14, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                 4
  CLUS_2               2                 0
  CLUS_3               2                 0
  CLUS_4               5                 1
  CLUS_5               2                 2
  CLUS_6               2                 0
[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"
