[1] "ofn"        "-oTDLBC-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/DLBC-TP/22541055/DLBC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/22573826/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=48, common to both=48
[1] "Reduce the number of clustering variables from 37 to 36."
[1] 36 48
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           10            38 
  B2M MUTATED B2M WILD-TYPE 
           10            38 
[1] "MYD88 MUTATION ANALYSIS"
[1] 3
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              45 
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              45 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             34 
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             34 
[1] "HLA-C MUTATION ANALYSIS"
[1] 3
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              41 
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              41 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               7               41 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               7               41 
[1] "CD79B MUTATION ANALYSIS"
[1] 3
  CD79B MUTATED CD79B WILD-TYPE 
              5              43 
  CD79B MUTATED CD79B WILD-TYPE 
              5              43 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             43 
  TP53 MUTATED TP53 WILD-TYPE 
             5             43 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                7                41 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                7                41 
[1] "TMSB4X MUTATION ANALYSIS"
[1] 3
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               6               42 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               6               42 
[1] "APLF MUTATION ANALYSIS"
[1] 3
  APLF MUTATED APLF WILD-TYPE 
             3             45 
  APLF MUTATED APLF WILD-TYPE 
             3             45 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              7              41 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              7              41 
[1] "CIITA MUTATION ANALYSIS"
[1] 3
  CIITA MUTATED CIITA WILD-TYPE 
              5              43 
  CIITA MUTATED CIITA WILD-TYPE 
              5              43 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
            4            44 
  KDR MUTATED KDR WILD-TYPE 
            4            44 
[1] "CARD11 MUTATION ANALYSIS"
[1] 3
  CARD11 MUTATED CARD11 WILD-TYPE 
              10               38 
  CARD11 MUTATED CARD11 WILD-TYPE 
              10               38 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             3             45 
  EZH2 MUTATED EZH2 WILD-TYPE 
             3             45 
[1] "NFKBIE MUTATION ANALYSIS"
[1] 3
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4               44 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4               44 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
             3             45 
  MLH1 MUTATED MLH1 WILD-TYPE 
             3             45 
[1] "FAS MUTATION ANALYSIS"
[1] 3
  FAS MUTATED FAS WILD-TYPE 
            5            43 
  FAS MUTATED FAS WILD-TYPE 
            5            43 
[1] "ENOX1 MUTATION ANALYSIS"
[1] 3
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              4              44 
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              4              44 
[1] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
             4             44 
  SGK1 MUTATED SGK1 WILD-TYPE 
             4             44 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               3               45 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               3               45 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
             3             45 
  APOB MUTATED APOB WILD-TYPE 
             3             45 
[1] "MCM8 MUTATION ANALYSIS"
[1] 3
  MCM8 MUTATED MCM8 WILD-TYPE 
             3             45 
  MCM8 MUTATED MCM8 WILD-TYPE 
             3             45 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               43 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               43 
[1] "PCDHA10 MUTATION ANALYSIS"
[1] 3
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                6                42 
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                6                42 
[1] "LRRC16B MUTATION ANALYSIS"
[1] 3
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                4                44 
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                4                44 
[1] "PNPLA7 MUTATION ANALYSIS"
[1] 3
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               3               45 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               3               45 
[1] "SLC16A8 MUTATION ANALYSIS"
[1] 3
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                3                45 
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                3                45 
[1] "PKHD1L1 MUTATION ANALYSIS"
[1] 3
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                5                43 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                5                43 
[1] "HRCT1 MUTATION ANALYSIS"
[1] 3
  HRCT1 MUTATED HRCT1 WILD-TYPE 
              4              44 
  HRCT1 MUTATED HRCT1 WILD-TYPE 
              4              44 
[1] "TYRO3 MUTATION ANALYSIS"
[1] 3
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              4              44 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              4              44 
[1] "GSTZ1 MUTATION ANALYSIS"
[1] 3
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              3              45 
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              3              45 
[1] "STAT3 MUTATION ANALYSIS"
[1] 3
  STAT3 MUTATED STAT3 WILD-TYPE 
              7              41 
  STAT3 MUTATED STAT3 WILD-TYPE 
              7              41 
[1] "IRF8 MUTATION ANALYSIS"
[1] 3
  IRF8 MUTATED IRF8 WILD-TYPE 
             5             43 
  IRF8 MUTATED IRF8 WILD-TYPE 
             5             43 
[1] "TMEM30A MUTATION ANALYSIS"
[1] 3
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                4                44 
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                4                44 
[1] "UBE2A MUTATION ANALYSIS"
[1] 3
  UBE2A MUTATED UBE2A WILD-TYPE 
              4              44 
  UBE2A MUTATED UBE2A WILD-TYPE 
              4              44 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 48 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	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 48 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = B2M MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  B2M MUTATED        7      2      1
  B2M WILD-TYPE     13      5     20
D1V1, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           7            13
  CLUS_2           2             5
  CLUS_3           1            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 CLUS_4
  B2M MUTATED        4      1      3      2
  B2M WILD-TYPE      5     12     16      5
D1V2, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           4             5
  CLUS_2           1            12
  CLUS_3           3            16
  CLUS_4           2             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  B2M MUTATED        0      1      1      1      3      1
  B2M WILD-TYPE      6      4      4      5      3      4
D1V3, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           0             6
  CLUS_2           1             4
  CLUS_3           1             4
  CLUS_4           1             5
  CLUS_5           3             3
  CLUS_6           1             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  B2M MUTATED        1      4      2
  B2M WILD-TYPE      5     11     10
D1V4, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             5
  CLUS_2           4            11
  CLUS_3           2            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  B2M MUTATED        4      0      1      0      3      2
  B2M WILD-TYPE      6     12      8      3      5      4
D1V5, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           4             6
  CLUS_2           0            12
  CLUS_3           1             8
  CLUS_4           0             3
  CLUS_5           3             5
  CLUS_6           2             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  B2M MUTATED        6      0      1      3
  B2M WILD-TYPE     16     11      6      5
D1V6, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           6            16
  CLUS_2           0            11
  CLUS_3           1             6
  CLUS_4           3             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  B2M MUTATED        4      4      1
  B2M WILD-TYPE     12     12     14
D1V7, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           4            12
  CLUS_2           4            12
  CLUS_3           1            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  B2M MUTATED        1      2      1      2      3
  B2M WILD-TYPE      8     10      7     10      3
D1V8, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             8
  CLUS_2           2            10
  CLUS_3           1             7
  CLUS_4           2            10
  CLUS_5           3             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  B2M MUTATED        1      2      0      5
  B2M WILD-TYPE      8      8      9      9
D1V9, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             8
  CLUS_2           2             8
  CLUS_3           0             9
  CLUS_4           5             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  B2M MUTATED        1      3      0      4
  B2M WILD-TYPE      7     12      5     10
D1V10, multiclass
        clus
vv       B2M MUTATED B2M WILD-TYPE
  CLUS_1           1             7
  CLUS_2           3            12
  CLUS_3           0             5
  CLUS_4           4            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MYD88 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MYD88 MUTATED        2      0      1
  MYD88 WILD-TYPE     18      7     20
D2V1, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             0               7
  CLUS_3             1              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 CLUS_4
  MYD88 MUTATED        0      0      3      0
  MYD88 WILD-TYPE      9     13     16      7
D2V2, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              13
  CLUS_3             3              16
  CLUS_4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MYD88 MUTATED        0      1      0      0      0      2
  MYD88 WILD-TYPE      6      4      5      6      6      3
D2V3, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             0               6
  CLUS_6             2               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MYD88 MUTATED        1      1      1
  MYD88 WILD-TYPE      5     14     11
D2V4, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1              14
  CLUS_3             1              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 CLUS_5 CLUS_6
  MYD88 MUTATED        1      0      2      0      0      0
  MYD88 WILD-TYPE      9     12      7      3      8      6
D2V5, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               9
  CLUS_2             0              12
  CLUS_3             2               7
  CLUS_4             0               3
  CLUS_5             0               8
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MYD88 MUTATED        0      0      2      1
  MYD88 WILD-TYPE     22     11      5      7
D2V6, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             0              22
  CLUS_2             0              11
  CLUS_3             2               5
  CLUS_4             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MYD88 MUTATED        1      0      2
  MYD88 WILD-TYPE     15     16     13
D2V7, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             0              16
  CLUS_3             2              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 CLUS_4 CLUS_5
  MYD88 MUTATED        1      0      1      1      0
  MYD88 WILD-TYPE      8     12      7     11      6
D2V8, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              12
  CLUS_3             1               7
  CLUS_4             1              11
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MYD88 MUTATED        1      0      2      0
  MYD88 WILD-TYPE      8     10      7     14
D2V9, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              10
  CLUS_3             2               7
  CLUS_4             0              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MYD88 MUTATED        0      0      1      2
  MYD88 WILD-TYPE      8     15      4     12
D2V10, multiclass
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0              15
  CLUS_3             1               4
  CLUS_4             2              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MLL2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        2      2     10
  MLL2 WILD-TYPE     18      5     11
D3V1, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            2              5
  CLUS_3           10             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
  MLL2 MUTATED        0      3      9      2
  MLL2 WILD-TYPE      9     10     10      5
D3V2, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            3             10
  CLUS_3            9             10
  CLUS_4            2              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MLL2 MUTATED        3      2      2      3      2      0
  MLL2 WILD-TYPE      3      3      3      3      4      5
D3V3, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            3              3
  CLUS_2            2              3
  CLUS_3            2              3
  CLUS_4            3              3
  CLUS_5            2              4
  CLUS_6            0              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        2      5      5
  MLL2 WILD-TYPE      4     10      7
D3V4, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              4
  CLUS_2            5             10
  CLUS_3            5              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MLL2 MUTATED        3      3      4      1      3      0
  MLL2 WILD-TYPE      7      9      5      2      5      6
D3V5, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            3              7
  CLUS_2            3              9
  CLUS_3            4              5
  CLUS_4            1              2
  CLUS_5            3              5
  CLUS_6            0              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        8      3      1      2
  MLL2 WILD-TYPE     14      8      6      6
D3V6, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            8             14
  CLUS_2            3              8
  CLUS_3            1              6
  CLUS_4            2              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        4      5      5
  MLL2 WILD-TYPE     12     11     10
D3V7, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             12
  CLUS_2            5             11
  CLUS_3            5             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL2 MUTATED        2      3      2      4      3
  MLL2 WILD-TYPE      7      9      6      8      3
D3V8, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            3              9
  CLUS_3            2              6
  CLUS_4            4              8
  CLUS_5            3              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        2      2      4      5
  MLL2 WILD-TYPE      7      8      5      9
D3V9, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            2              8
  CLUS_3            4              5
  CLUS_4            5              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        2      2      4      5
  MLL2 WILD-TYPE      6     13      1      9
D3V10, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            2             13
  CLUS_3            4              1
  CLUS_4            5              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = HLA-C MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-C MUTATED        4      2      1
  HLA-C WILD-TYPE     16      5     20
D4V1, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             4              16
  CLUS_2             2               5
  CLUS_3             1              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 CLUS_4
  HLA-C MUTATED        2      3      2      0
  HLA-C WILD-TYPE      7     10     17      7
D4V2, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             2               7
  CLUS_2             3              10
  CLUS_3             2              17
  CLUS_4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HLA-C MUTATED        1      1      0      1      2      0
  HLA-C WILD-TYPE      5      4      5      5      4      5
D4V3, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               4
  CLUS_6             0               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-C MUTATED        1      3      1
  HLA-C WILD-TYPE      5     12     11
D4V4, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             1               5
  CLUS_2             3              12
  CLUS_3             1              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 CLUS_5 CLUS_6
  HLA-C MUTATED        1      3      1      0      1      1
  HLA-C WILD-TYPE      9      9      8      3      7      5
D4V5, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             1               9
  CLUS_2             3               9
  CLUS_3             1               8
  CLUS_4             0               3
  CLUS_5             1               7
  CLUS_6             1               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-C MUTATED        3      3      0      1
  HLA-C WILD-TYPE     19      8      7      7
D4V6, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             3              19
  CLUS_2             3               8
  CLUS_3             0               7
  CLUS_4             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HLA-C MUTATED        1      5      1
  HLA-C WILD-TYPE     15     11     14
D4V7, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             1              15
  CLUS_2             5              11
  CLUS_3             1              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HLA-C MUTATED        2      4      0      1      0
  HLA-C WILD-TYPE      7      8      8     11      6
D4V8, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             2               7
  CLUS_2             4               8
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-C MUTATED        0      3      1      3
  HLA-C WILD-TYPE      9      7      8     11
D4V9, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3               7
  CLUS_3             1               8
  CLUS_4             3              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HLA-C MUTATED        0      5      1      1
  HLA-C WILD-TYPE      8     10      4     13
D4V10, multiclass
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  CLUS_1             0               8
  CLUS_2             5              10
  CLUS_3             1               4
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = ZNF814 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        2      0      5
  ZNF814 WILD-TYPE     18      7     16
D5V1, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              0                7
  CLUS_3              5               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 CLUS_4
  ZNF814 MUTATED        1      3      3      0
  ZNF814 WILD-TYPE      8     10     16      7
D5V2, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              3               10
  CLUS_3              3               16
  CLUS_4              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZNF814 MUTATED        0      0      0      3      0      0
  ZNF814 WILD-TYPE      6      5      5      3      6      5
D5V3, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              3                3
  CLUS_5              0                6
  CLUS_6              0                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        0      3      0
  ZNF814 WILD-TYPE      6     12     12
D5V4, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              3               12
  CLUS_3              0               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZNF814 MUTATED        0      3      3      0      0      1
  ZNF814 WILD-TYPE     10      9      6      3      8      5
D5V5, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               10
  CLUS_2              3                9
  CLUS_3              3                6
  CLUS_4              0                3
  CLUS_5              0                8
  CLUS_6              1                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        0      3      1      3
  ZNF814 WILD-TYPE     22      8      6      5
D5V6, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0               22
  CLUS_2              3                8
  CLUS_3              1                6
  CLUS_4              3                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZNF814 MUTATED        2      1      4
  ZNF814 WILD-TYPE     14     15     11
D5V7, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1               15
  CLUS_3              4               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 CLUS_5
  ZNF814 MUTATED        0      1      0      6      0
  ZNF814 WILD-TYPE      9     11      8      6      6
D5V8, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1               11
  CLUS_3              0                8
  CLUS_4              6                6
  CLUS_5              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        0      2      3      1
  ZNF814 WILD-TYPE      9      8      6     13
D5V9, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2                8
  CLUS_3              3                6
  CLUS_4              1               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZNF814 MUTATED        0      4      2      0
  ZNF814 WILD-TYPE      8     11      3     14
D5V10, multiclass
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              4               11
  CLUS_3              2                3
  CLUS_4              0               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = CD79B MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD79B MUTATED        1      0      4
  CD79B WILD-TYPE     19      7     17
D6V1, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             1              19
  CLUS_2             0               7
  CLUS_3             4              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD79B MUTATED        0      1      4      0
  CD79B WILD-TYPE      9     12     15      7
D6V2, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              12
  CLUS_3             4              15
  CLUS_4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CD79B MUTATED        0      1      1      0      0      1
  CD79B WILD-TYPE      6      4      4      6      6      4
D6V3, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               6
  CLUS_2             1               4
  CLUS_3             1               4
  CLUS_4             0               6
  CLUS_5             0               6
  CLUS_6             1               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD79B MUTATED        0      0      3
  CD79B WILD-TYPE      6     15      9
D6V4, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0              15
  CLUS_3             3               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CD79B MUTATED        0      1      3      0      1      0
  CD79B WILD-TYPE     10     11      6      3      7      6
D6V5, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0              10
  CLUS_2             1              11
  CLUS_3             3               6
  CLUS_4             0               3
  CLUS_5             1               7
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD79B MUTATED        2      1      0      2
  CD79B WILD-TYPE     20     10      7      6
D6V6, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2              20
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             2               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD79B MUTATED        2      0      3
  CD79B WILD-TYPE     14     16     12
D6V7, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2              14
  CLUS_2             0              16
  CLUS_3             3              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CD79B MUTATED        0      1      2      2      0
  CD79B WILD-TYPE      9     11      6     10      6
D6V8, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              11
  CLUS_3             2               6
  CLUS_4             2              10
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD79B MUTATED        2      0      1      0
  CD79B WILD-TYPE      7     10      8     14
D6V9, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2               7
  CLUS_2             0              10
  CLUS_3             1               8
  CLUS_4             0              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD79B MUTATED        2      0      1      0
  CD79B WILD-TYPE      6     15      4     14
D6V10, multiclass
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  CLUS_1             2               6
  CLUS_2             0              15
  CLUS_3             1               4
  CLUS_4             0              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        1      0      4
  TP53 WILD-TYPE     19      7     17
D7V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             19
  CLUS_2            0              7
  CLUS_3            4             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        0      0      3      2
  TP53 WILD-TYPE      9     13     16      5
D7V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            0             13
  CLUS_3            3             16
  CLUS_4            2              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        2      0      0      0      0      0
  TP53 WILD-TYPE      4      5      5      6      6      5
D7V3, multiclass
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A86F 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8046     TCGA-FF-8047 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR     TCGA-FF-A7CW 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6325     TCGA-G8-6326 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G8-6906     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        1      1      0
  TP53 WILD-TYPE      5     14     12
D7V4, multiclass
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A86F 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8046     TCGA-FF-8047 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR     TCGA-FF-A7CW 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6325     TCGA-G8-6326 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-G8-6906     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        0      0      1      1      3      0
  TP53 WILD-TYPE     10     12      8      2      5      6
D7V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             10
  CLUS_2            0             12
  CLUS_3            1              8
  CLUS_4            1              2
  CLUS_5            3              5
  CLUS_6            0              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        4      0      1      0
  TP53 WILD-TYPE     18     11      6      8
D7V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             18
  CLUS_2            0             11
  CLUS_3            1              6
  CLUS_4            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2      3      0
  TP53 WILD-TYPE     14     13     15
D7V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            3             13
  CLUS_3            0             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 CLUS_4 CLUS_5
  TP53 MUTATED        1      1      2      0      1
  TP53 WILD-TYPE      8     11      6     12      5
D7V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1             11
  CLUS_3            2              6
  CLUS_4            0             12
  CLUS_5            1              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        2      0      0      2
  TP53 WILD-TYPE      7     10      9     12
D7V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            0             10
  CLUS_3            0              9
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        2      0      0      2
  TP53 WILD-TYPE      6     15      5     12
D7V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            0             15
  CLUS_3            0              5
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = TNFAIP3 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TNFAIP3 MUTATED        5      0      2
  TNFAIP3 WILD-TYPE     15      7     19
D8V1, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               5                15
  CLUS_2               0                 7
  CLUS_3               2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNFAIP3 MUTATED        2      3      2      0
  TNFAIP3 WILD-TYPE      7     10     17      7
D8V2, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                10
  CLUS_3               2                17
  CLUS_4               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TNFAIP3 MUTATED        0      2      0      0      3      1
  TNFAIP3 WILD-TYPE      6      3      5      6      3      4
D8V3, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               2                 3
  CLUS_3               0                 5
  CLUS_4               0                 6
  CLUS_5               3                 3
  CLUS_6               1                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TNFAIP3 MUTATED        0      4      2
  TNFAIP3 WILD-TYPE      6     11     10
D8V4, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               4                11
  CLUS_3               2                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TNFAIP3 MUTATED        0      2      2      0      1      2
  TNFAIP3 WILD-TYPE     10     10      7      3      7      4
D8V5, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                10
  CLUS_2               2                10
  CLUS_3               2                 7
  CLUS_4               0                 3
  CLUS_5               1                 7
  CLUS_6               2                 4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNFAIP3 MUTATED        2      2      1      2
  TNFAIP3 WILD-TYPE     20      9      6      6
D8V6, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               2                20
  CLUS_2               2                 9
  CLUS_3               1                 6
  CLUS_4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TNFAIP3 MUTATED        0      3      4
  TNFAIP3 WILD-TYPE     16     13     11
D8V7, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               3                13
  CLUS_3               4                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 CLUS_5
  TNFAIP3 MUTATED        2      3      0      1      1
  TNFAIP3 WILD-TYPE      7      9      8     11      5
D8V8, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               3                 9
  CLUS_3               0                 8
  CLUS_4               1                11
  CLUS_5               1                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNFAIP3 MUTATED        0      2      2      2
  TNFAIP3 WILD-TYPE      9      8      7     12
D8V9, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                 8
  CLUS_3               2                 7
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TNFAIP3 MUTATED        0      4      1      1
  TNFAIP3 WILD-TYPE      8     11      4     13
D8V10, multiclass
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               4                11
  CLUS_3               1                 4
  CLUS_4               1                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = TMSB4X MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TMSB4X MUTATED        2      3      1
  TMSB4X WILD-TYPE     18      4     20
D9V1, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              2               18
  CLUS_2              3                4
  CLUS_3              1               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 CLUS_4
  TMSB4X MUTATED        3      1      1      1
  TMSB4X WILD-TYPE      6     12     18      6
D9V2, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              3                6
  CLUS_2              1               12
  CLUS_3              1               18
  CLUS_4              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TMSB4X MUTATED        0      2      1      2      0      0
  TMSB4X WILD-TYPE      6      3      4      4      6      5
D9V3, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2                3
  CLUS_3              1                4
  CLUS_4              2                4
  CLUS_5              0                6
  CLUS_6              0                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TMSB4X MUTATED        0      2      3
  TMSB4X WILD-TYPE      6     13      9
D9V4, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2               13
  CLUS_3              3                9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TMSB4X MUTATED        2      1      0      0      1      2
  TMSB4X WILD-TYPE      8     11      9      3      7      4
D9V5, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              2                8
  CLUS_2              1               11
  CLUS_3              0                9
  CLUS_4              0                3
  CLUS_5              1                7
  CLUS_6              2                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMSB4X MUTATED        3      1      0      2
  TMSB4X WILD-TYPE     19     10      7      6
D9V6, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              3               19
  CLUS_2              1               10
  CLUS_3              0                7
  CLUS_4              2                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TMSB4X MUTATED        2      3      1
  TMSB4X WILD-TYPE     14     13     14
D9V7, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              2               14
  CLUS_2              3               13
  CLUS_3              1               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TMSB4X MUTATED        1      3      0      1      1
  TMSB4X WILD-TYPE      8      9      8     11      5
D9V8, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1                8
  CLUS_2              3                9
  CLUS_3              0                8
  CLUS_4              1               11
  CLUS_5              1                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMSB4X MUTATED        0      3      0      3
  TMSB4X WILD-TYPE      9      7      9     11
D9V9, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3                7
  CLUS_3              0                9
  CLUS_4              3               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMSB4X MUTATED        1      3      0      2
  TMSB4X WILD-TYPE      7     12      5     12
D9V10, multiclass
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  CLUS_1              1                7
  CLUS_2              3               12
  CLUS_3              0                5
  CLUS_4              2               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = APLF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APLF MUTATED        3      0      0
  APLF WILD-TYPE     17      7     21
D10V1, multiclass
        clus
vv       APLF MUTATED APLF WILD-TYPE
  CLUS_1            3             17
  CLUS_2            0              7
  CLUS_3            0             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 CLUS_4
  APLF MUTATED        2      0      1      0
  APLF WILD-TYPE      7     13     18      7
D10V2, multiclass
        clus
vv       APLF MUTATED APLF WILD-TYPE
  CLUS_1            2              7
  CLUS_2            0             13
  CLUS_3            1             18
  CLUS_4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APLF MUTATED        0      0      0      0      1      0
  APLF WILD-TYPE      6      5      5      6      5      5
D10V3, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             1             32 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6326     TCGA-G8-6914     TCGA-GS-A9TT 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TV     TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APLF MUTATED        0      1      0
  APLF WILD-TYPE      6     14     12
D10V4, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             1             32 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6326     TCGA-G8-6914     TCGA-GS-A9TT 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TV     TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APLF MUTATED        2      0      0      0      1      0
  APLF WILD-TYPE      8     12      9      3      7      6
D10V5, multiclass
        clus
vv       APLF MUTATED APLF WILD-TYPE
  CLUS_1            2              8
  CLUS_2            0             12
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            1              7
  CLUS_6            0              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APLF MUTATED        3      0      0      0
  APLF WILD-TYPE     19     11      7      8
D10V6, multiclass
        clus
vv       APLF MUTATED APLF WILD-TYPE
  CLUS_1            3             19
  CLUS_2            0             11
  CLUS_3            0              7
  CLUS_4            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APLF MUTATED        1      1      0
  APLF WILD-TYPE     15     15     15
D10V7, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             2             45 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6325     TCGA-G8-6326 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-G8-6907     TCGA-G8-6914     TCGA-GR-7353     TCGA-GR-A4D4 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GR-A4D5     TCGA-GR-A4D6     TCGA-GR-A4D9     TCGA-GS-A9TQ 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV     TCGA-GS-A9TW 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TX     TCGA-GS-A9TY     TCGA-GS-A9TZ     TCGA-GS-A9U3 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-VB-A8QN 
"APLF WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APLF MUTATED        1      1      0      0      0
  APLF WILD-TYPE      8     11      8     12      6
D10V8, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             2             45 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6325     TCGA-G8-6326 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-G8-6907     TCGA-G8-6914     TCGA-GR-7353     TCGA-GR-A4D4 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GR-A4D5     TCGA-GR-A4D6     TCGA-GR-A4D9     TCGA-GS-A9TQ 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV     TCGA-GS-A9TW 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TX     TCGA-GS-A9TY     TCGA-GS-A9TZ     TCGA-GS-A9U3 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-VB-A8QN 
"APLF WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APLF MUTATED        0      0      0      2
  APLF WILD-TYPE      9     10      9     12
D10V9, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             2             40 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6324 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6326     TCGA-G8-6907     TCGA-G8-6914 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TQ     TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9U3     TCGA-GS-A9U4 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APLF MUTATED        0      1      0      1
  APLF WILD-TYPE      8     14      5     13
D10V10, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             2             40 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6324 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6326     TCGA-G8-6907     TCGA-G8-6914 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TQ     TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9U3     TCGA-GS-A9U4 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 

Clustering(11) Variable = RHPN2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RHPN2 MUTATED        4      1      2
  RHPN2 WILD-TYPE     16      6     19
D11V1, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             1               6
  CLUS_3             2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RHPN2 MUTATED        1      2      1      3
  RHPN2 WILD-TYPE      8     11     18      4
D11V2, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              11
  CLUS_3             1              18
  CLUS_4             3               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RHPN2 MUTATED        0      0      0      1      2      0
  RHPN2 WILD-TYPE      6      5      5      5      4      5
D11V3, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               4
  CLUS_6             0               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RHPN2 MUTATED        0      3      0
  RHPN2 WILD-TYPE      6     12     12
D11V4, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3              12
  CLUS_3             0              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RHPN2 MUTATED        3      3      0      0      1      0
  RHPN2 WILD-TYPE      7      9      9      3      7      6
D11V5, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             3               7
  CLUS_2             3               9
  CLUS_3             0               9
  CLUS_4             0               3
  CLUS_5             1               7
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RHPN2 MUTATED        5      2      0      0
  RHPN2 WILD-TYPE     17      9      7      8
D11V6, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             5              17
  CLUS_2             2               9
  CLUS_3             0               7
  CLUS_4             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  RHPN2 MUTATED        2      3      1
  RHPN2 WILD-TYPE     14     13     14
D11V7, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             3              13
  CLUS_3             1              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RHPN2 MUTATED        3      1      0      1      1
  RHPN2 WILD-TYPE      6     11      8     11      5
D11V8, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             1              11
  CLUS_3             0               8
  CLUS_4             1              11
  CLUS_5             1               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RHPN2 MUTATED        1      0      1      4
  RHPN2 WILD-TYPE      8     10      8     10
D11V9, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              10
  CLUS_3             1               8
  CLUS_4             4              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RHPN2 MUTATED        0      2      0      4
  RHPN2 WILD-TYPE      8     13      5     10
D11V10, multiclass
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             2              13
  CLUS_3             0               5
  CLUS_4             4              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = CIITA MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CIITA MUTATED        4      0      1
  CIITA WILD-TYPE     16      7     20
D12V1, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             4              16
  CLUS_2             0               7
  CLUS_3             1              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 CLUS_4
  CIITA MUTATED        2      0      3      0
  CIITA WILD-TYPE      7     13     16      7
D12V2, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             2               7
  CLUS_2             0              13
  CLUS_3             3              16
  CLUS_4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CIITA MUTATED        0      0      1      1      1      0
  CIITA WILD-TYPE      6      5      4      5      5      5
D12V3, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             1               5
  CLUS_5             1               5
  CLUS_6             0               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CIITA MUTATED        0      2      1
  CIITA WILD-TYPE      6     13     11
D12V4, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2              13
  CLUS_3             1              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 CLUS_5 CLUS_6
  CIITA MUTATED        1      0      2      1      1      0
  CIITA WILD-TYPE      9     12      7      2      7      6
D12V5, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             1               9
  CLUS_2             0              12
  CLUS_3             2               7
  CLUS_4             1               2
  CLUS_5             1               7
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CIITA MUTATED        2      0      2      1
  CIITA WILD-TYPE     20     11      5      7
D12V6, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             2              20
  CLUS_2             0              11
  CLUS_3             2               5
  CLUS_4             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CIITA MUTATED        3      1      0
  CIITA WILD-TYPE     13     15     15
D12V7, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             3              13
  CLUS_2             1              15
  CLUS_3             0              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 CLUS_4 CLUS_5
  CIITA MUTATED        0      0      1      2      1
  CIITA WILD-TYPE      9     12      7     10      5
D12V8, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              12
  CLUS_3             1               7
  CLUS_4             2              10
  CLUS_5             1               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CIITA MUTATED        0      0      2      1
  CIITA WILD-TYPE      9     10      7     13
D12V9, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              10
  CLUS_3             2               7
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CIITA MUTATED        0      1      1      1
  CIITA WILD-TYPE      8     14      4     13
D12V10, multiclass
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1              14
  CLUS_3             1               4
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = KDR MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        2      1      1
  KDR WILD-TYPE     18      6     20
D13V1, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           2            18
  CLUS_2           1             6
  CLUS_3           1            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 CLUS_4
  KDR MUTATED        1      2      1      0
  KDR WILD-TYPE      8     11     18      7
D13V2, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1             8
  CLUS_2           2            11
  CLUS_3           1            18
  CLUS_4           0             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KDR MUTATED        0      0      0      0      0      2
  KDR WILD-TYPE      6      5      5      6      6      3
D13V3, multiclass
[1] "Remove cluster labels:" "KDR MUTATED"           
clus
  KDR MUTATED KDR WILD-TYPE 
            2            31 
   TCGA-FA-8693    TCGA-FA-A4BB    TCGA-FA-A4XK    TCGA-FA-A6HN    TCGA-FA-A6HO 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-FA-A7DS    TCGA-FA-A7Q1    TCGA-FA-A82F    TCGA-FA-A86F    TCGA-FF-8041 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-FF-8042    TCGA-FF-8043    TCGA-FF-8046    TCGA-FF-8047    TCGA-FF-8061 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-FF-8062    TCGA-FF-A7CR    TCGA-FF-A7CW    TCGA-FF-A7CX    TCGA-FM-8000 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-G8-6325    TCGA-G8-6906    TCGA-G8-6914    TCGA-GS-A9TT    TCGA-GS-A9TV 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-GS-A9TW    TCGA-GS-A9TX    TCGA-GS-A9TZ    TCGA-GS-A9U4    TCGA-RQ-A6JB 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-VB-A8QN 
"KDR WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        1      0      1
  KDR WILD-TYPE      5     15     11
D13V4, multiclass
[1] "Remove cluster labels:" "KDR MUTATED"           
clus
  KDR MUTATED KDR WILD-TYPE 
            2            31 
   TCGA-FA-8693    TCGA-FA-A4BB    TCGA-FA-A4XK    TCGA-FA-A6HN    TCGA-FA-A6HO 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-FA-A7DS    TCGA-FA-A7Q1    TCGA-FA-A82F    TCGA-FA-A86F    TCGA-FF-8041 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-FF-8042    TCGA-FF-8043    TCGA-FF-8046    TCGA-FF-8047    TCGA-FF-8061 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-FF-8062    TCGA-FF-A7CR    TCGA-FF-A7CW    TCGA-FF-A7CX    TCGA-FM-8000 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-G8-6325    TCGA-G8-6906    TCGA-G8-6914    TCGA-GS-A9TT    TCGA-GS-A9TV 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-GS-A9TW    TCGA-GS-A9TX    TCGA-GS-A9TZ    TCGA-GS-A9U4    TCGA-RQ-A6JB 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-VB-A8QN 
"KDR WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KDR MUTATED        0      1      1      0      1      1
  KDR WILD-TYPE     10     11      8      3      7      5
D13V5, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           0            10
  CLUS_2           1            11
  CLUS_3           1             8
  CLUS_4           0             3
  CLUS_5           1             7
  CLUS_6           1             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        3      1      0      0
  KDR WILD-TYPE     19     10      7      8
D13V6, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           3            19
  CLUS_2           1            10
  CLUS_3           0             7
  CLUS_4           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        2      1      1
  KDR WILD-TYPE     14     15     14
D13V7, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           2            14
  CLUS_2           1            15
  CLUS_3           1            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KDR MUTATED        1      2      1      0      0
  KDR WILD-TYPE      8     10      7     12      6
D13V8, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1             8
  CLUS_2           2            10
  CLUS_3           1             7
  CLUS_4           0            12
  CLUS_5           0             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        1      2      0      1
  KDR WILD-TYPE      8      8      9     13
D13V9, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1             8
  CLUS_2           2             8
  CLUS_3           0             9
  CLUS_4           1            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        1      3      0      0
  KDR WILD-TYPE      7     12      5     14
D13V10, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1             7
  CLUS_2           3            12
  CLUS_3           0             5
  CLUS_4           0            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = CARD11 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CARD11 MUTATED        4      1      5
  CARD11 WILD-TYPE     16      6     16
D14V1, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              4               16
  CLUS_2              1                6
  CLUS_3              5               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 CLUS_4
  CARD11 MUTATED        2      2      3      3
  CARD11 WILD-TYPE      7     11     16      4
D14V2, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              2               11
  CLUS_3              3               16
  CLUS_4              3                4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CARD11 MUTATED        0      0      1      2      2      1
  CARD11 WILD-TYPE      6      5      4      4      4      4
D14V3, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0                5
  CLUS_3              1                4
  CLUS_4              2                4
  CLUS_5              2                4
  CLUS_6              1                4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CARD11 MUTATED        0      4      2
  CARD11 WILD-TYPE      6     11     10
D14V4, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              4               11
  CLUS_3              2               10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CARD11 MUTATED        4      2      1      1      2      0
  CARD11 WILD-TYPE      6     10      8      2      6      6
D14V5, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              4                6
  CLUS_2              2               10
  CLUS_3              1                8
  CLUS_4              1                2
  CLUS_5              2                6
  CLUS_6              0                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CARD11 MUTATED        6      2      2      0
  CARD11 WILD-TYPE     16      9      5      8
D14V6, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              6               16
  CLUS_2              2                9
  CLUS_3              2                5
  CLUS_4              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CARD11 MUTATED        3      4      2
  CARD11 WILD-TYPE     13     12     13
D14V7, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              4               12
  CLUS_3              2               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 CLUS_4 CLUS_5
  CARD11 MUTATED        4      2      1      1      1
  CARD11 WILD-TYPE      5     10      7     11      5
D14V8, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              4                5
  CLUS_2              2               10
  CLUS_3              1                7
  CLUS_4              1               11
  CLUS_5              1                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CARD11 MUTATED        1      0      2      5
  CARD11 WILD-TYPE      8     10      7      9
D14V9, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              0               10
  CLUS_3              2                7
  CLUS_4              5                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CARD11 MUTATED        1      2      1      4
  CARD11 WILD-TYPE      7     13      4     10
D14V10, multiclass
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  CLUS_1              1                7
  CLUS_2              2               13
  CLUS_3              1                4
  CLUS_4              4               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = EZH2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EZH2 MUTATED        2      1      0
  EZH2 WILD-TYPE     18      6     21
D15V1, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            1              6
  CLUS_3            0             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 CLUS_4
  EZH2 MUTATED        0      1      1      1
  EZH2 WILD-TYPE      9     12     18      6
D15V2, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1             12
  CLUS_3            1             18
  CLUS_4            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  EZH2 MUTATED        0      0      0      0      2      0
  EZH2 WILD-TYPE      6      5      5      6      4      5
D15V3, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-G8-6326 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-G8-6906     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EZH2 MUTATED        0      2      0
  EZH2 WILD-TYPE      6     13     12
D15V4, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-G8-6326 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-G8-6906     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  EZH2 MUTATED        0      0      0      0      2      1
  EZH2 WILD-TYPE     10     12      9      3      6      5
D15V5, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0             10
  CLUS_2            0             12
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            2              6
  CLUS_6            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EZH2 MUTATED        3      0      0      0
  EZH2 WILD-TYPE     19     11      7      8
D15V6, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            3             19
  CLUS_2            0             11
  CLUS_3            0              7
  CLUS_4            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EZH2 MUTATED        0      3      0
  EZH2 WILD-TYPE     16     13     15
D15V7, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0             16
  CLUS_2            3             13
  CLUS_3            0             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 CLUS_4 CLUS_5
  EZH2 MUTATED        1      0      0      0      2
  EZH2 WILD-TYPE      8     12      8     12      4
D15V8, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            0             12
  CLUS_3            0              8
  CLUS_4            0             12
  CLUS_5            2              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EZH2 MUTATED        0      1      0      2
  EZH2 WILD-TYPE      9      9      9     12
D15V9, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1              9
  CLUS_3            0              9
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EZH2 MUTATED        0      1      0      2
  EZH2 WILD-TYPE      8     14      5     12
D15V10, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1             14
  CLUS_3            0              5
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = NFKBIE MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFKBIE MUTATED        2      0      2
  NFKBIE WILD-TYPE     18      7     19
D16V1, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              2               18
  CLUS_2              0                7
  CLUS_3              2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFKBIE MUTATED        1      1      0      2
  NFKBIE WILD-TYPE      8     12     19      5
D16V2, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1               12
  CLUS_3              0               19
  CLUS_4              2                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NFKBIE MUTATED        0      0      0      0      2      0
  NFKBIE WILD-TYPE      6      5      5      6      4      5
D16V3, multiclass
[1] "Remove cluster labels:" "NFKBIE MUTATED"        
clus
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               2               31 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FF-8046       TCGA-FF-8047       TCGA-FF-8062       TCGA-FF-A7CR 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000       TCGA-G8-6326 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G8-6906       TCGA-G8-6914       TCGA-GS-A9TT       TCGA-GS-A9TV 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFKBIE MUTATED        0      2      0
  NFKBIE WILD-TYPE      6     13     12
D16V4, multiclass
[1] "Remove cluster labels:" "NFKBIE MUTATED"        
clus
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               2               31 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FF-8046       TCGA-FF-8047       TCGA-FF-8062       TCGA-FF-A7CR 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000       TCGA-G8-6326 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G8-6906       TCGA-G8-6914       TCGA-GS-A9TT       TCGA-GS-A9TV 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NFKBIE MUTATED        1      1      0      0      1      1
  NFKBIE WILD-TYPE      9     11      9      3      7      5
D16V5, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              1                9
  CLUS_2              1               11
  CLUS_3              0                9
  CLUS_4              0                3
  CLUS_5              1                7
  CLUS_6              1                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFKBIE MUTATED        3      1      0      0
  NFKBIE WILD-TYPE     19     10      7      8
D16V6, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              3               19
  CLUS_2              1               10
  CLUS_3              0                7
  CLUS_4              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFKBIE MUTATED        1      3      0
  NFKBIE WILD-TYPE     15     13     15
D16V7, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              1               15
  CLUS_2              3               13
  CLUS_3              0               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 CLUS_4 CLUS_5
  NFKBIE MUTATED        2      2      0      0      0
  NFKBIE WILD-TYPE      7     10      8     12      6
D16V8, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              2                7
  CLUS_2              2               10
  CLUS_3              0                8
  CLUS_4              0               12
  CLUS_5              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFKBIE MUTATED        0      1      0      3
  NFKBIE WILD-TYPE      9      9      9     11
D16V9, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1                9
  CLUS_3              0                9
  CLUS_4              3               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFKBIE MUTATED        0      2      0      2
  NFKBIE WILD-TYPE      8     13      5     12
D16V10, multiclass
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  CLUS_1              0                8
  CLUS_2              2               13
  CLUS_3              0                5
  CLUS_4              2               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = MLH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLH1 MUTATED        3      0      0
  MLH1 WILD-TYPE     17      7     21
D17V1, multiclass
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  CLUS_1            3             17
  CLUS_2            0              7
  CLUS_3            0             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 CLUS_4
  MLH1 MUTATED        1      1      1      0
  MLH1 WILD-TYPE      8     12     18      7
D17V2, multiclass
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1             12
  CLUS_3            1             18
  CLUS_4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MLH1 MUTATED        0      0      0      0      2      0
  MLH1 WILD-TYPE      6      5      5      6      4      5
D17V3, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-G8-6326     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLH1 MUTATED        0      2      0
  MLH1 WILD-TYPE      6     13     12
D17V4, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-G8-6326     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MLH1 MUTATED        2      0      0      0      0      1
  MLH1 WILD-TYPE      8     12      9      3      8      5
D17V5, multiclass
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  CLUS_1            2              8
  CLUS_2            0             12
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            0              8
  CLUS_6            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLH1 MUTATED        3      0      0      0
  MLH1 WILD-TYPE     19     11      7      8
D17V6, multiclass
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  CLUS_1            3             19
  CLUS_2            0             11
  CLUS_3            0              7
  CLUS_4            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLH1 MUTATED        1      1      0
  MLH1 WILD-TYPE     15     15     15
D17V7, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             45 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6326     TCGA-G8-6907 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-G8-6909     TCGA-G8-6914     TCGA-GR-7353     TCGA-GR-A4D4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GR-A4D5     TCGA-GR-A4D6     TCGA-GR-A4D9     TCGA-GS-A9TQ 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV     TCGA-GS-A9TW 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TX     TCGA-GS-A9TY     TCGA-GS-A9TZ     TCGA-GS-A9U3 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VB-A8QN 
"MLH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLH1 MUTATED        2      0      0      0      0
  MLH1 WILD-TYPE      7     12      8     12      6
D17V8, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             45 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6326     TCGA-G8-6907 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-G8-6909     TCGA-G8-6914     TCGA-GR-7353     TCGA-GR-A4D4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GR-A4D5     TCGA-GR-A4D6     TCGA-GR-A4D9     TCGA-GS-A9TQ 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV     TCGA-GS-A9TW 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TX     TCGA-GS-A9TY     TCGA-GS-A9TZ     TCGA-GS-A9U3 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9U4     TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-VB-A8QN 
"MLH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLH1 MUTATED        0      1      0      1
  MLH1 WILD-TYPE      9      9      9     13
D17V9, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             40 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6324 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-G8-6326     TCGA-G8-6907     TCGA-G8-6909     TCGA-G8-6914 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TQ     TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9U3     TCGA-GS-A9U4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLH1 MUTATED        0      1      0      1
  MLH1 WILD-TYPE      8     14      5     13
D17V10, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             40 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062     TCGA-FF-A7CR 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6324 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-G8-6326     TCGA-G8-6907     TCGA-G8-6909     TCGA-G8-6914 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GR-7353     TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D6 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TQ     TCGA-GS-A9TT     TCGA-GS-A9TU     TCGA-GS-A9TV 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9U3     TCGA-GS-A9U4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 

Clustering(18) Variable = FAS MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  FAS MUTATED        2      1      2
  FAS WILD-TYPE     18      6     19
D18V1, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           2            18
  CLUS_2           1             6
  CLUS_3           2            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAS MUTATED        1      1      1      2
  FAS WILD-TYPE      8     12     18      5
D18V2, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           1             8
  CLUS_2           1            12
  CLUS_3           1            18
  CLUS_4           2             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FAS MUTATED        0      0      1      0      0      0
  FAS WILD-TYPE      6      5      4      6      6      5
D18V3, multiclass
[1] "Remove cluster labels:" "FAS MUTATED"           
clus
  FAS MUTATED FAS WILD-TYPE 
            1            32 
   TCGA-FA-8693    TCGA-FA-A4BB    TCGA-FA-A4XK    TCGA-FA-A6HN    TCGA-FA-A6HO 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FA-A7DS    TCGA-FA-A82F    TCGA-FA-A86F    TCGA-FF-8041    TCGA-FF-8042 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FF-8043    TCGA-FF-8046    TCGA-FF-8047    TCGA-FF-8061    TCGA-FF-8062 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FF-A7CR    TCGA-FF-A7CW    TCGA-FF-A7CX    TCGA-FM-8000    TCGA-G8-6325 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-G8-6326    TCGA-G8-6906    TCGA-G8-6914    TCGA-GS-A9TT    TCGA-GS-A9TV 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-GS-A9TW    TCGA-GS-A9TX    TCGA-GS-A9TZ    TCGA-GS-A9U4    TCGA-RQ-A68N 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-RQ-A6JB    TCGA-VB-A8QN 
"FAS WILD-TYPE" "FAS WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  FAS MUTATED        0      0      1
  FAS WILD-TYPE      6     15     11
D18V4, multiclass
[1] "Remove cluster labels:" "FAS MUTATED"           
clus
  FAS MUTATED FAS WILD-TYPE 
            1            32 
   TCGA-FA-8693    TCGA-FA-A4BB    TCGA-FA-A4XK    TCGA-FA-A6HN    TCGA-FA-A6HO 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FA-A7DS    TCGA-FA-A82F    TCGA-FA-A86F    TCGA-FF-8041    TCGA-FF-8042 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FF-8043    TCGA-FF-8046    TCGA-FF-8047    TCGA-FF-8061    TCGA-FF-8062 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FF-A7CR    TCGA-FF-A7CW    TCGA-FF-A7CX    TCGA-FM-8000    TCGA-G8-6325 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-G8-6326    TCGA-G8-6906    TCGA-G8-6914    TCGA-GS-A9TT    TCGA-GS-A9TV 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-GS-A9TW    TCGA-GS-A9TX    TCGA-GS-A9TZ    TCGA-GS-A9U4    TCGA-RQ-A68N 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-RQ-A6JB    TCGA-VB-A8QN 
"FAS WILD-TYPE" "FAS WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FAS MUTATED        0      1      0      2      2      0
  FAS WILD-TYPE     10     11      9      1      6      6
D18V5, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           0            10
  CLUS_2           1            11
  CLUS_3           0             9
  CLUS_4           2             1
  CLUS_5           2             6
  CLUS_6           0             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAS MUTATED        2      1      2      0
  FAS WILD-TYPE     20     10      5      8
D18V6, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           2            20
  CLUS_2           1            10
  CLUS_3           2             5
  CLUS_4           0             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  FAS MUTATED        1      3      1
  FAS WILD-TYPE     15     13     14
D18V7, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           1            15
  CLUS_2           3            13
  CLUS_3           1            14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAS MUTATED        1      1      1      1      1
  FAS WILD-TYPE      8     11      7     11      5
D18V8, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           1             8
  CLUS_2           1            11
  CLUS_3           1             7
  CLUS_4           1            11
  CLUS_5           1             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAS MUTATED        0      1      1      3
  FAS WILD-TYPE      9      9      8     11
D18V9, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           0             9
  CLUS_2           1             9
  CLUS_3           1             8
  CLUS_4           3            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAS MUTATED        0      2      0      3
  FAS WILD-TYPE      8     13      5     11
D18V10, multiclass
        clus
vv       FAS MUTATED FAS WILD-TYPE
  CLUS_1           0             8
  CLUS_2           2            13
  CLUS_3           0             5
  CLUS_4           3            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = ENOX1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ENOX1 MUTATED        3      0      1
  ENOX1 WILD-TYPE     17      7     20
D19V1, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             0               7
  CLUS_3             1              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 CLUS_4
  ENOX1 MUTATED        1      1      2      0
  ENOX1 WILD-TYPE      8     12     17      7
D19V2, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              12
  CLUS_3             2              17
  CLUS_4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ENOX1 MUTATED        0      0      0      1      2      0
  ENOX1 WILD-TYPE      6      5      5      5      4      5
D19V3, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               4
  CLUS_6             0               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ENOX1 MUTATED        0      3      0
  ENOX1 WILD-TYPE      6     12     12
D19V4, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3              12
  CLUS_3             0              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ENOX1 MUTATED        2      1      0      0      0      1
  ENOX1 WILD-TYPE      8     11      9      3      8      5
D19V5, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             2               8
  CLUS_2             1              11
  CLUS_3             0               9
  CLUS_4             0               3
  CLUS_5             0               8
  CLUS_6             1               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ENOX1 MUTATED        2      1      0      1
  ENOX1 WILD-TYPE     20     10      7      7
D19V6, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             1               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ENOX1 MUTATED        2      1      1
  ENOX1 WILD-TYPE     14     15     14
D19V7, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             1              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ENOX1 MUTATED        2      2      0      0      0
  ENOX1 WILD-TYPE      7     10      8     12      6
D19V8, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             2              10
  CLUS_3             0               8
  CLUS_4             0              12
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ENOX1 MUTATED        0      0      0      3
  ENOX1 WILD-TYPE      9     10      9     11
D19V9, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              10
  CLUS_3             0               9
  CLUS_4             3              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ENOX1 MUTATED        0      1      0      2
  ENOX1 WILD-TYPE      8     14      5     12
D19V10, multiclass
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1              14
  CLUS_3             0               5
  CLUS_4             2              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = SGK1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SGK1 MUTATED        4      0      0
  SGK1 WILD-TYPE     16      7     21
D20V1, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            4             16
  CLUS_2            0              7
  CLUS_3            0             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 CLUS_4
  SGK1 MUTATED        4      0      0      0
  SGK1 WILD-TYPE      5     13     19      7
D20V2, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            4              5
  CLUS_2            0             13
  CLUS_3            0             19
  CLUS_4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SGK1 MUTATED        1      0      1      0      0      0
  SGK1 WILD-TYPE      5      5      4      6      6      5
D20V3, multiclass
[1] "Remove cluster labels:" "SGK1 MUTATED"          
clus
  SGK1 MUTATED SGK1 WILD-TYPE 
             2             31 
    TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN     TCGA-FA-A6HO 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-A7CR     TCGA-FF-A7CW 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6325     TCGA-G8-6326 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-G8-6906     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SGK1 MUTATED        1      0      1
  SGK1 WILD-TYPE      5     15     11
D20V4, multiclass
[1] "Remove cluster labels:" "SGK1 MUTATED"          
clus
  SGK1 MUTATED SGK1 WILD-TYPE 
             2             31 
    TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN     TCGA-FA-A6HO 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F     TCGA-FA-A86F 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043     TCGA-FF-8046 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-A7CR     TCGA-FF-A7CW 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-FF-A7CX     TCGA-FM-8000     TCGA-G8-6325     TCGA-G8-6326 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-G8-6906     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"SGK1 WILD-TYPE" "SGK1 WILD-TYPE" "SGK1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SGK1 MUTATED        3      0      0      0      1      0
  SGK1 WILD-TYPE      7     12      9      3      7      6
D20V5, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            3              7
  CLUS_2            0             12
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            1              7
  CLUS_6            0              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SGK1 MUTATED        4      0      0      0
  SGK1 WILD-TYPE     18     11      7      8
D20V6, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            4             18
  CLUS_2            0             11
  CLUS_3            0              7
  CLUS_4            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SGK1 MUTATED        1      2      0
  SGK1 WILD-TYPE     15     14     15
D20V7, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1             15
  CLUS_2            2             14
  CLUS_3            0             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 CLUS_4 CLUS_5
  SGK1 MUTATED        1      2      0      0      0
  SGK1 WILD-TYPE      8     10      8     12      6
D20V8, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             10
  CLUS_3            0              8
  CLUS_4            0             12
  CLUS_5            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SGK1 MUTATED        1      0      0      2
  SGK1 WILD-TYPE      8     10      9     12
D20V9, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            0             10
  CLUS_3            0              9
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SGK1 MUTATED        2      1      0      0
  SGK1 WILD-TYPE      6     14      5     14
D20V10, multiclass
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  CLUS_1            2              6
  CLUS_2            1             14
  CLUS_3            0              5
  CLUS_4            0             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = IFITM3 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFITM3 MUTATED        2      0      1
  IFITM3 WILD-TYPE     18      7     20
D21V1, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              0                7
  CLUS_3              1               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 CLUS_4
  IFITM3 MUTATED        0      1      0      2
  IFITM3 WILD-TYPE      9     12     19      5
D21V2, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1               12
  CLUS_3              0               19
  CLUS_4              2                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IFITM3 MUTATED        1      0      0      1      0      0
  IFITM3 WILD-TYPE      5      5      5      5      6      5
D21V3, multiclass
[1] "Remove cluster labels:" "IFITM3 MUTATED"        
clus
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               2               31 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8047 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR       TCGA-FF-A7CW 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FF-A7CX       TCGA-FM-8000       TCGA-G8-6325       TCGA-G8-6326 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-G8-6906       TCGA-G8-6914       TCGA-GS-A9TT       TCGA-GS-A9TV 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFITM3 MUTATED        0      2      0
  IFITM3 WILD-TYPE      6     13     12
D21V4, multiclass
[1] "Remove cluster labels:" "IFITM3 MUTATED"        
clus
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               2               31 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FA-A86F       TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8047 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR       TCGA-FF-A7CW 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FF-A7CX       TCGA-FM-8000       TCGA-G8-6325       TCGA-G8-6326 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-G8-6906       TCGA-G8-6914       TCGA-GS-A9TT       TCGA-GS-A9TV 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IFITM3 MUTATED        0      2      0      0      1      0
  IFITM3 WILD-TYPE     10     10      9      3      7      6
D21V5, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              0               10
  CLUS_2              2               10
  CLUS_3              0                9
  CLUS_4              0                3
  CLUS_5              1                7
  CLUS_6              0                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IFITM3 MUTATED        2      1      0      0
  IFITM3 WILD-TYPE     20     10      7      8
D21V6, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              2               20
  CLUS_2              1               10
  CLUS_3              0                7
  CLUS_4              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IFITM3 MUTATED        0      3      0
  IFITM3 WILD-TYPE     16     13     15
D21V7, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              0               16
  CLUS_2              3               13
  CLUS_3              0               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 CLUS_4 CLUS_5
  IFITM3 MUTATED        1      1      0      0      1
  IFITM3 WILD-TYPE      8     11      8     12      5
D21V8, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1               11
  CLUS_3              0                8
  CLUS_4              0               12
  CLUS_5              1                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IFITM3 MUTATED        1      0      0      2
  IFITM3 WILD-TYPE      8     10      9     12
D21V9, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              0               10
  CLUS_3              0                9
  CLUS_4              2               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IFITM3 MUTATED        0      1      0      2
  IFITM3 WILD-TYPE      8     14      5     12
D21V10, multiclass
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              1               14
  CLUS_3              0                5
  CLUS_4              2               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = APOB MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        2      1      0
  APOB WILD-TYPE     18      6     21
D22V1, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            2             18
  CLUS_2            1              6
  CLUS_3            0             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 CLUS_4
  APOB MUTATED        1      1      0      1
  APOB WILD-TYPE      8     12     19      6
D22V2, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1             12
  CLUS_3            0             19
  CLUS_4            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APOB MUTATED        0      0      0      2      0      0
  APOB WILD-TYPE      6      5      5      4      6      5
D22V3, multiclass
[1] "Remove cluster labels:" "APOB MUTATED"          
clus
  APOB MUTATED APOB WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6326     TCGA-G8-6906     TCGA-GS-A9TT 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-GS-A9TV     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        0      1      1
  APOB WILD-TYPE      6     14     11
D22V4, multiclass
[1] "Remove cluster labels:" "APOB MUTATED"          
clus
  APOB MUTATED APOB WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6326     TCGA-G8-6906     TCGA-GS-A9TT 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-GS-A9TV     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  APOB MUTATED        1      1      0      0      0      1
  APOB WILD-TYPE      9     11      9      3      8      5
D22V5, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1              9
  CLUS_2            1             11
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            0              8
  CLUS_6            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOB MUTATED        1      1      0      1
  APOB WILD-TYPE     21     10      7      7
D22V6, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1             21
  CLUS_2            1             10
  CLUS_3            0              7
  CLUS_4            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  APOB MUTATED        2      1      0
  APOB WILD-TYPE     14     15     15
D22V7, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             15
  CLUS_3            0             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 CLUS_4 CLUS_5
  APOB MUTATED        0      1      1      1      0
  APOB WILD-TYPE      9     11      7     11      6
D22V8, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1             11
  CLUS_3            1              7
  CLUS_4            1             11
  CLUS_5            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOB MUTATED        1      1      0      1
  APOB WILD-TYPE      8      9      9     13
D22V9, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1              9
  CLUS_3            0              9
  CLUS_4            1             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APOB MUTATED        1      2      0      0
  APOB WILD-TYPE      7     13      5     14
D22V10, multiclass
        clus
vv       APOB MUTATED APOB WILD-TYPE
  CLUS_1            1              7
  CLUS_2            2             13
  CLUS_3            0              5
  CLUS_4            0             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = MCM8 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM8 MUTATED        2      1      0
  MCM8 WILD-TYPE     18      6     21
D23V1, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            1              6
  CLUS_3            0             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 CLUS_4
  MCM8 MUTATED        0      2      1      0
  MCM8 WILD-TYPE      9     11     18      7
D23V2, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             11
  CLUS_3            1             18
  CLUS_4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MCM8 MUTATED        0      0      0      0      1      1
  MCM8 WILD-TYPE      6      5      5      6      5      4
D23V3, multiclass
[1] "Remove cluster labels:" "MCM8 MUTATED"          
clus
  MCM8 MUTATED MCM8 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM8 MUTATED        1      1      0
  MCM8 WILD-TYPE      5     14     12
D23V4, multiclass
[1] "Remove cluster labels:" "MCM8 MUTATED"          
clus
  MCM8 MUTATED MCM8 WILD-TYPE 
             2             31 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A6HN 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FA-A6HO     TCGA-FA-A7DS     TCGA-FA-A7Q1     TCGA-FA-A82F 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FA-A86F     TCGA-FF-8041     TCGA-FF-8042     TCGA-FF-8043 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FF-8046     TCGA-FF-8047     TCGA-FF-8061     TCGA-FF-8062 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX     TCGA-FM-8000 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-G8-6325     TCGA-G8-6914     TCGA-GS-A9TT     TCGA-GS-A9TV 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-GS-A9TW     TCGA-GS-A9TX     TCGA-GS-A9TZ     TCGA-GS-A9U4 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-VB-A8QN 
"MCM8 WILD-TYPE" "MCM8 WILD-TYPE" "MCM8 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MCM8 MUTATED        1      1      0      0      0      1
  MCM8 WILD-TYPE      9     11      9      3      8      5
D23V5, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            1              9
  CLUS_2            1             11
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            0              8
  CLUS_6            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MCM8 MUTATED        2      1      0      0
  MCM8 WILD-TYPE     20     10      7      8
D23V6, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            1             10
  CLUS_3            0              7
  CLUS_4            0              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MCM8 MUTATED        2      1      0
  MCM8 WILD-TYPE     14     15     15
D23V7, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             15
  CLUS_3            0             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 CLUS_4 CLUS_5
  MCM8 MUTATED        2      1      0      0      0
  MCM8 WILD-TYPE      7     11      8     12      6
D23V8, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            1             11
  CLUS_3            0              8
  CLUS_4            0             12
  CLUS_5            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MCM8 MUTATED        0      1      0      2
  MCM8 WILD-TYPE      9      9      9     12
D23V9, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1              9
  CLUS_3            0              9
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MCM8 MUTATED        0      2      0      1
  MCM8 WILD-TYPE      8     13      5     13
D23V10, multiclass
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            2             13
  CLUS_3            0              5
  CLUS_4            1             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      0      2
  ARID1A WILD-TYPE     17      7     19
D24V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               17
  CLUS_2              0                7
  CLUS_3              2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      2      2      1
  ARID1A WILD-TYPE      9     11     17      6
D24V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2               11
  CLUS_3              2               17
  CLUS_4              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARID1A MUTATED        0      1      0      0      1      0
  ARID1A WILD-TYPE      6      4      5      6      5      5
D24V3, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               31 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-G8-6325       TCGA-G8-6326 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-G8-6906       TCGA-G8-6914       TCGA-GS-A9TT       TCGA-GS-A9TV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      1      1
  ARID1A WILD-TYPE      6     14     11
D24V4, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               31 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A6HN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FA-A6HO       TCGA-FA-A7DS       TCGA-FA-A7Q1       TCGA-FA-A82F 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-8041       TCGA-FF-8042       TCGA-FF-8043       TCGA-FF-8046 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-8047       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CR 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-G8-6325       TCGA-G8-6326 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-G8-6906       TCGA-G8-6914       TCGA-GS-A9TT       TCGA-GS-A9TV 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-GS-A9TW       TCGA-GS-A9TX       TCGA-GS-A9TZ       TCGA-GS-A9U4 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-VB-A8QN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARID1A MUTATED        0      2      1      1      1      0
  ARID1A WILD-TYPE     10     10      8      2      7      6
D24V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               10
  CLUS_2              2               10
  CLUS_3              1                8
  CLUS_4              1                2
  CLUS_5              1                7
  CLUS_6              0                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        1      2      1      1
  ARID1A WILD-TYPE     21      9      6      7
D24V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               21
  CLUS_2              2                9
  CLUS_3              1                6
  CLUS_4              1                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      3      1
  ARID1A WILD-TYPE     15     13     14
D24V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               15
  CLUS_2              3               13
  CLUS_3              1               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        1      2      0      1      1
  ARID1A WILD-TYPE      8     10      8     11      5
D24V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               10
  CLUS_3              0                8
  CLUS_4              1               11
  CLUS_5              1                5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      1      0      3
  ARID1A WILD-TYPE      9      9      9     11
D24V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1                9
  CLUS_3              0                9
  CLUS_4              3               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      2      0      2
  ARID1A WILD-TYPE      8     13      5     12
D24V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                8
  CLUS_2              2               13
  CLUS_3              0                5
  CLUS_4              2               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = PCDHA10 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHA10 MUTATED        1      3      2
  PCDHA10 WILD-TYPE     19      4     19
D25V1, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               1                19
  CLUS_2               3                 4
  CLUS_3               2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHA10 MUTATED        2      1      0      3
  PCDHA10 WILD-TYPE      7     12     19      4
D25V2, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               1                12
  CLUS_3               0                19
  CLUS_4               3                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCDHA10 MUTATED        0      0      0      1      1      0
  PCDHA10 WILD-TYPE      6      5      5      5      5      5
D25V3, multiclass
[1] "Remove cluster labels:" "PCDHA10 MUTATED"       
clus
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                2                31 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8062        TCGA-FF-A7CR 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6325 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-GS-A9TT        TCGA-GS-A9TV 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ        TCGA-GS-A9U4 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHA10 MUTATED        0      1      1
  PCDHA10 WILD-TYPE      6     14     11
D25V4, multiclass
[1] "Remove cluster labels:" "PCDHA10 MUTATED"       
clus
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                2                31 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8062        TCGA-FF-A7CR 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6325 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-GS-A9TT        TCGA-GS-A9TV 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ        TCGA-GS-A9U4 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCDHA10 MUTATED        2      1      0      0      3      0
  PCDHA10 WILD-TYPE      8     11      9      3      5      6
D25V5, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               2                 8
  CLUS_2               1                11
  CLUS_3               0                 9
  CLUS_4               0                 3
  CLUS_5               3                 5
  CLUS_6               0                 6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHA10 MUTATED        5      1      0      0
  PCDHA10 WILD-TYPE     17     10      7      8
D25V6, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               5                17
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHA10 MUTATED        2      3      1
  PCDHA10 WILD-TYPE     14     13     14
D25V7, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                13
  CLUS_3               1                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCDHA10 MUTATED        1      1      1      1      2
  PCDHA10 WILD-TYPE      8     11      7     11      4
D25V8, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                11
  CLUS_3               1                 7
  CLUS_4               1                11
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHA10 MUTATED        1      1      0      4
  PCDHA10 WILD-TYPE      8      9      9     10
D25V9, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 9
  CLUS_3               0                 9
  CLUS_4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHA10 MUTATED        1      2      0      3
  PCDHA10 WILD-TYPE      7     13      5     11
D25V10, multiclass
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               2                13
  CLUS_3               0                 5
  CLUS_4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = LRRC16B MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  LRRC16B MUTATED        1      3      0
  LRRC16B WILD-TYPE     19      4     21
D26V1, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               1                19
  CLUS_2               3                 4
  CLUS_3               0                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 CLUS_4
  LRRC16B MUTATED        2      0      0      2
  LRRC16B WILD-TYPE      7     13     19      5
D26V2, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                13
  CLUS_3               0                19
  CLUS_4               2                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LRRC16B MUTATED        0      0      0      1      0      0
  LRRC16B WILD-TYPE      6      5      5      5      6      5
D26V3, multiclass
[1] "Remove cluster labels:" "LRRC16B MUTATED"       
clus
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                1                32 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-GS-A9TT 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  LRRC16B MUTATED        0      0      1
  LRRC16B WILD-TYPE      6     15     11
D26V4, multiclass
[1] "Remove cluster labels:" "LRRC16B MUTATED"       
clus
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                1                32 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-G8-6325        TCGA-G8-6326        TCGA-G8-6906        TCGA-GS-A9TT 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LRRC16B MUTATED        2      0      0      0      2      0
  LRRC16B WILD-TYPE      8     12      9      3      6      6
D26V5, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               2                 8
  CLUS_2               0                12
  CLUS_3               0                 9
  CLUS_4               0                 3
  CLUS_5               2                 6
  CLUS_6               0                 6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC16B MUTATED        4      0      0      0
  LRRC16B WILD-TYPE     18     11      7      8
D26V6, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               4                18
  CLUS_2               0                11
  CLUS_3               0                 7
  CLUS_4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  LRRC16B MUTATED        1      2      0
  LRRC16B WILD-TYPE     15     14     15
D26V7, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                14
  CLUS_3               0                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 CLUS_4 CLUS_5
  LRRC16B MUTATED        0      0      1      0      2
  LRRC16B WILD-TYPE      9     12      7     12      4
D26V8, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                12
  CLUS_3               1                 7
  CLUS_4               0                12
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC16B MUTATED        1      0      0      2
  LRRC16B WILD-TYPE      8     10      9     12
D26V9, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                10
  CLUS_3               0                 9
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC16B MUTATED        1      0      0      2
  LRRC16B WILD-TYPE      7     15      5     12
D26V10, multiclass
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               0                15
  CLUS_3               0                 5
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = PNPLA7 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PNPLA7 MUTATED        2      1      0
  PNPLA7 WILD-TYPE     18      6     21
D27V1, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              2               18
  CLUS_2              1                6
  CLUS_3              0               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 CLUS_4
  PNPLA7 MUTATED        0      1      1      1
  PNPLA7 WILD-TYPE      9     12     18      6
D27V2, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1               12
  CLUS_3              1               18
  CLUS_4              1                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PNPLA7 MUTATED        0      0      0      1      2      0
  PNPLA7 WILD-TYPE      6      5      5      5      4      5
D27V3, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0                5
  CLUS_3              0                5
  CLUS_4              1                5
  CLUS_5              2                4
  CLUS_6              0                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PNPLA7 MUTATED        0      2      1
  PNPLA7 WILD-TYPE      6     13     11
D27V4, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2               13
  CLUS_3              1               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 CLUS_5 CLUS_6
  PNPLA7 MUTATED        2      0      0      0      0      1
  PNPLA7 WILD-TYPE      8     12      9      3      8      5
D27V5, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              2                8
  CLUS_2              0               12
  CLUS_3              0                9
  CLUS_4              0                3
  CLUS_5              0                8
  CLUS_6              1                5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PNPLA7 MUTATED        3      0      0      0
  PNPLA7 WILD-TYPE     19     11      7      8
D27V6, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              3               19
  CLUS_2              0               11
  CLUS_3              0                7
  CLUS_4              0                8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PNPLA7 MUTATED        2      1      0
  PNPLA7 WILD-TYPE     14     15     15
D27V7, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1               15
  CLUS_3              0               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 CLUS_4 CLUS_5
  PNPLA7 MUTATED        2      0      1      0      0
  PNPLA7 WILD-TYPE      7     12      7     12      6
D27V8, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              0               12
  CLUS_3              1                7
  CLUS_4              0               12
  CLUS_5              0                6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PNPLA7 MUTATED        1      1      0      1
  PNPLA7 WILD-TYPE      8      9      9     13
D27V9, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1                9
  CLUS_3              0                9
  CLUS_4              1               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PNPLA7 MUTATED        1      1      0      1
  PNPLA7 WILD-TYPE      7     14      5     13
D27V10, multiclass
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  CLUS_1              1                7
  CLUS_2              1               14
  CLUS_3              0                5
  CLUS_4              1               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = SLC16A8 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC16A8 MUTATED        1      2      0
  SLC16A8 WILD-TYPE     19      5     21
D28V1, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                 5
  CLUS_3               0                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 CLUS_4
  SLC16A8 MUTATED        1      1      0      1
  SLC16A8 WILD-TYPE      8     12     19      6
D28V2, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                12
  CLUS_3               0                19
  CLUS_4               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SLC16A8 MUTATED        0      0      0      0      1      0
  SLC16A8 WILD-TYPE      6      5      5      6      5      5
D28V3, multiclass
[1] "Remove cluster labels:" "SLC16A8 MUTATED"       
clus
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                1                32 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6914        TCGA-GS-A9TT 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC16A8 MUTATED        0      1      0
  SLC16A8 WILD-TYPE      6     14     12
D28V4, multiclass
[1] "Remove cluster labels:" "SLC16A8 MUTATED"       
clus
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                1                32 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8041        TCGA-FF-8042        TCGA-FF-8043 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FF-8046        TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6914        TCGA-GS-A9TT 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9TZ 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
       TCGA-GS-A9U4        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" "SLC16A8 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SLC16A8 MUTATED        0      0      0      0      2      1
  SLC16A8 WILD-TYPE     10     12      9      3      6      5
D28V5, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               0                10
  CLUS_2               0                12
  CLUS_3               0                 9
  CLUS_4               0                 3
  CLUS_5               2                 6
  CLUS_6               1                 5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC16A8 MUTATED        3      0      0      0
  SLC16A8 WILD-TYPE     19     11      7      8
D28V6, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               3                19
  CLUS_2               0                11
  CLUS_3               0                 7
  CLUS_4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC16A8 MUTATED        0      3      0
  SLC16A8 WILD-TYPE     16     13     15
D28V7, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               3                13
  CLUS_3               0                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 CLUS_4 CLUS_5
  SLC16A8 MUTATED        1      0      0      0      2
  SLC16A8 WILD-TYPE      8     12      8     12      4
D28V8, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                12
  CLUS_3               0                 8
  CLUS_4               0                12
  CLUS_5               2                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC16A8 MUTATED        0      1      0      2
  SLC16A8 WILD-TYPE      9      9      9     12
D28V9, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                 9
  CLUS_3               0                 9
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC16A8 MUTATED        0      1      0      2
  SLC16A8 WILD-TYPE      8     14      5     12
D28V10, multiclass
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               1                14
  CLUS_3               0                 5
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = PKHD1L1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PKHD1L1 MUTATED        3      2      0
  PKHD1L1 WILD-TYPE     17      5     21
D29V1, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               3                17
  CLUS_2               2                 5
  CLUS_3               0                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 CLUS_4
  PKHD1L1 MUTATED        3      1      0      1
  PKHD1L1 WILD-TYPE      6     12     19      6
D29V2, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               3                 6
  CLUS_2               1                12
  CLUS_3               0                19
  CLUS_4               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PKHD1L1 MUTATED        0      0      0      0      2      0
  PKHD1L1 WILD-TYPE      6      5      5      6      4      5
D29V3, multiclass
[1] "Remove cluster labels:" "PKHD1L1 MUTATED"       
clus
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                2                31 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6325 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6914        TCGA-GS-A9TT 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9U4 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PKHD1L1 MUTATED        0      2      0
  PKHD1L1 WILD-TYPE      6     13     12
D29V4, multiclass
[1] "Remove cluster labels:" "PKHD1L1 MUTATED"       
clus
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                2                31 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A6HN 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FA-A6HO        TCGA-FA-A7DS        TCGA-FA-A7Q1        TCGA-FA-A82F 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FA-A86F        TCGA-FF-8042        TCGA-FF-8043        TCGA-FF-8046 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FF-8047        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CR 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6325 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-G8-6914        TCGA-GS-A9TT 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-GS-A9TV        TCGA-GS-A9TW        TCGA-GS-A9TX        TCGA-GS-A9U4 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PKHD1L1 MUTATED        0      1      0      0      3      1
  PKHD1L1 WILD-TYPE     10     11      9      3      5      5
D29V5, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               0                10
  CLUS_2               1                11
  CLUS_3               0                 9
  CLUS_4               0                 3
  CLUS_5               3                 5
  CLUS_6               1                 5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PKHD1L1 MUTATED        3      1      0      1
  PKHD1L1 WILD-TYPE     19     10      7      7
D29V6, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               3                19
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PKHD1L1 MUTATED        0      4      1
  PKHD1L1 WILD-TYPE     16     12     14
D29V7, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               0                16
  CLUS_2               4                12
  CLUS_3               1                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PKHD1L1 MUTATED        0      2      0      0      3
  PKHD1L1 WILD-TYPE      9     10      8     12      3
D29V8, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                10
  CLUS_3               0                 8
  CLUS_4               0                12
  CLUS_5               3                 3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PKHD1L1 MUTATED        0      0      0      4
  PKHD1L1 WILD-TYPE      9     10      9     10
D29V9, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                10
  CLUS_3               0                 9
  CLUS_4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PKHD1L1 MUTATED        0      2      0      2
  PKHD1L1 WILD-TYPE      8     13      5     12
D29V10, multiclass
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               2                13
  CLUS_3               0                 5
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = HRCT1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HRCT1 MUTATED        3      0      1
  HRCT1 WILD-TYPE     17      7     20
D30V1, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             0               7
  CLUS_3             1              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 CLUS_4
  HRCT1 MUTATED        0      1      1      2
  HRCT1 WILD-TYPE      9     12     18      5
D30V2, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              12
  CLUS_3             1              18
  CLUS_4             2               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HRCT1 MUTATED        0      0      0      1      2      0
  HRCT1 WILD-TYPE      6      5      5      5      4      5
D30V3, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               4
  CLUS_6             0               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HRCT1 MUTATED        0      3      0
  HRCT1 WILD-TYPE      6     12     12
D30V4, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3              12
  CLUS_3             0              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HRCT1 MUTATED        2      2      0      0      0      0
  HRCT1 WILD-TYPE      8     10      9      3      8      6
D30V5, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             2               8
  CLUS_2             2              10
  CLUS_3             0               9
  CLUS_4             0               3
  CLUS_5             0               8
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRCT1 MUTATED        3      1      0      0
  HRCT1 WILD-TYPE     19     10      7      8
D30V6, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             1              10
  CLUS_3             0               7
  CLUS_4             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  HRCT1 MUTATED        2      2      0
  HRCT1 WILD-TYPE     14     14     15
D30V7, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             2              14
  CLUS_3             0              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 CLUS_4 CLUS_5
  HRCT1 MUTATED        3      1      0      0      0
  HRCT1 WILD-TYPE      6     11      8     12      6
D30V8, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             1              11
  CLUS_3             0               8
  CLUS_4             0              12
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRCT1 MUTATED        1      0      0      3
  HRCT1 WILD-TYPE      8     10      9     11
D30V9, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              10
  CLUS_3             0               9
  CLUS_4             3              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRCT1 MUTATED        0      1      0      3
  HRCT1 WILD-TYPE      8     14      5     11
D30V10, multiclass
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1              14
  CLUS_3             0               5
  CLUS_4             3              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = TYRO3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TYRO3 MUTATED        3      1      0
  TYRO3 WILD-TYPE     17      6     21
D31V1, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             1               6
  CLUS_3             0              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 CLUS_4
  TYRO3 MUTATED        0      1      2      1
  TYRO3 WILD-TYPE      9     12     17      6
D31V2, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              12
  CLUS_3             2              17
  CLUS_4             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TYRO3 MUTATED        0      0      0      1      2      1
  TYRO3 WILD-TYPE      6      5      5      5      4      4
D31V3, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0               5
  CLUS_3             0               5
  CLUS_4             1               5
  CLUS_5             2               4
  CLUS_6             1               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TYRO3 MUTATED        0      3      1
  TYRO3 WILD-TYPE      6     12     11
D31V4, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             3              12
  CLUS_3             1              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 CLUS_5 CLUS_6
  TYRO3 MUTATED        2      0      1      0      0      1
  TYRO3 WILD-TYPE      8     12      8      3      8      5
D31V5, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             2               8
  CLUS_2             0              12
  CLUS_3             1               8
  CLUS_4             0               3
  CLUS_5             0               8
  CLUS_6             1               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TYRO3 MUTATED        3      0      1      0
  TYRO3 WILD-TYPE     19     11      6      8
D31V6, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             0              11
  CLUS_3             1               6
  CLUS_4             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TYRO3 MUTATED        2      1      1
  TYRO3 WILD-TYPE     14     15     14
D31V7, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             1              15
  CLUS_3             1              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TYRO3 MUTATED        3      0      1      0      0
  TYRO3 WILD-TYPE      6     12      7     12      6
D31V8, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             3               6
  CLUS_2             0              12
  CLUS_3             1               7
  CLUS_4             0              12
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TYRO3 MUTATED        1      1      1      1
  TYRO3 WILD-TYPE      8      9      8     13
D31V9, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1               9
  CLUS_3             1               8
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TYRO3 MUTATED        1      1      0      2
  TYRO3 WILD-TYPE      7     14      5     12
D31V10, multiclass
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             1              14
  CLUS_3             0               5
  CLUS_4             2              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = GSTZ1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GSTZ1 MUTATED        1      2      0
  GSTZ1 WILD-TYPE     19      5     21
D32V1, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             2               5
  CLUS_3             0              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 CLUS_4
  GSTZ1 MUTATED        0      1      0      2
  GSTZ1 WILD-TYPE      9     12     19      5
D32V2, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              12
  CLUS_3             0              19
  CLUS_4             2               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GSTZ1 MUTATED        0      0      0      1      1      0
  GSTZ1 WILD-TYPE      6      5      5      5      5      5
D32V3, multiclass
[1] "Remove cluster labels:" "GSTZ1 MUTATED"         
clus
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              2              31 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FA-A86F      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FF-A7CR      TCGA-FF-A7CW      TCGA-FF-A7CX      TCGA-FM-8000 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-G8-6326      TCGA-G8-6906      TCGA-GS-A9TT      TCGA-GS-A9TV 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ      TCGA-GS-A9U4 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GSTZ1 MUTATED        0      1      1
  GSTZ1 WILD-TYPE      6     14     11
D32V4, multiclass
[1] "Remove cluster labels:" "GSTZ1 MUTATED"         
clus
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              2              31 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A6HN 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FA-A6HO      TCGA-FA-A7DS      TCGA-FA-A7Q1      TCGA-FA-A82F 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FA-A86F      TCGA-FF-8041      TCGA-FF-8042      TCGA-FF-8043 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FF-8046      TCGA-FF-8047      TCGA-FF-8061      TCGA-FF-8062 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-FF-A7CR      TCGA-FF-A7CW      TCGA-FF-A7CX      TCGA-FM-8000 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-G8-6326      TCGA-G8-6906      TCGA-GS-A9TT      TCGA-GS-A9TV 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-GS-A9TW      TCGA-GS-A9TX      TCGA-GS-A9TZ      TCGA-GS-A9U4 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
     TCGA-RQ-A68N      TCGA-RQ-A6JB      TCGA-VB-A8QN 
"GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" "GSTZ1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GSTZ1 MUTATED        1      0      0      0      1      1
  GSTZ1 WILD-TYPE      9     12      9      3      7      5
D32V5, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             1               9
  CLUS_2             0              12
  CLUS_3             0               9
  CLUS_4             0               3
  CLUS_5             1               7
  CLUS_6             1               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GSTZ1 MUTATED        3      0      0      0
  GSTZ1 WILD-TYPE     19     11      7      8
D32V6, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             0              11
  CLUS_3             0               7
  CLUS_4             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  GSTZ1 MUTATED        1      2      0
  GSTZ1 WILD-TYPE     15     14     15
D32V7, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              14
  CLUS_3             0              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 CLUS_4 CLUS_5
  GSTZ1 MUTATED        1      0      1      0      1
  GSTZ1 WILD-TYPE      8     12      7     12      5
D32V8, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              12
  CLUS_3             1               7
  CLUS_4             0              12
  CLUS_5             1               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GSTZ1 MUTATED        1      1      0      1
  GSTZ1 WILD-TYPE      8      9      9     13
D32V9, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1               9
  CLUS_3             0               9
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GSTZ1 MUTATED        1      1      0      1
  GSTZ1 WILD-TYPE      7     14      5     13
D32V10, multiclass
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             1              14
  CLUS_3             0               5
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = STAT3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAT3 MUTATED        4      1      2
  STAT3 WILD-TYPE     16      6     19
D33V1, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             1               6
  CLUS_3             2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAT3 MUTATED        2      0      4      1
  STAT3 WILD-TYPE      7     13     15      6
D33V2, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             0              13
  CLUS_3             4              15
  CLUS_4             1               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  STAT3 MUTATED        1      1      0      0      1      2
  STAT3 WILD-TYPE      5      4      5      6      5      3
D33V3, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             1               4
  CLUS_3             0               5
  CLUS_4             0               6
  CLUS_5             1               5
  CLUS_6             2               3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAT3 MUTATED        1      2      2
  STAT3 WILD-TYPE      5     13     10
D33V4, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             1               5
  CLUS_2             2              13
  CLUS_3             2              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  STAT3 MUTATED        4      1      1      0      1      0
  STAT3 WILD-TYPE      6     11      8      3      7      6
D33V5, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             4               6
  CLUS_2             1              11
  CLUS_3             1               8
  CLUS_4             0               3
  CLUS_5             1               7
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAT3 MUTATED        5      1      1      0
  STAT3 WILD-TYPE     17     10      6      8
D33V6, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             5              17
  CLUS_2             1              10
  CLUS_3             1               6
  CLUS_4             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAT3 MUTATED        5      1      0
  STAT3 WILD-TYPE     11     15     15
D33V7, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             5              11
  CLUS_2             1              15
  CLUS_3             0              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 CLUS_4 CLUS_5
  STAT3 MUTATED        1      1      4      0      0
  STAT3 WILD-TYPE      8     11      4     12      6
D33V8, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              11
  CLUS_3             4               4
  CLUS_4             0              12
  CLUS_5             0               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAT3 MUTATED        4      1      0      1
  STAT3 WILD-TYPE      5      9      9     13
D33V9, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             4               5
  CLUS_2             1               9
  CLUS_3             0               9
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAT3 MUTATED        3      1      0      2
  STAT3 WILD-TYPE      5     14      5     12
D33V10, multiclass
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  CLUS_1             3               5
  CLUS_2             1              14
  CLUS_3             0               5
  CLUS_4             2              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = IRF8 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF8 MUTATED        4      0      1
  IRF8 WILD-TYPE     16      7     20
D34V1, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            4             16
  CLUS_2            0              7
  CLUS_3            1             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 CLUS_4
  IRF8 MUTATED        2      0      3      0
  IRF8 WILD-TYPE      7     13     16      7
D34V2, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            0             13
  CLUS_3            3             16
  CLUS_4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IRF8 MUTATED        0      0      0      0      2      1
  IRF8 WILD-TYPE      6      5      5      6      4      4
D34V3, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            0              5
  CLUS_3            0              5
  CLUS_4            0              6
  CLUS_5            2              4
  CLUS_6            1              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF8 MUTATED        1      2      0
  IRF8 WILD-TYPE      5     13     12
D34V4, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            2             13
  CLUS_3            0             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IRF8 MUTATED        2      0      0      0      2      1
  IRF8 WILD-TYPE      8     12      9      3      6      5
D34V5, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            2              8
  CLUS_2            0             12
  CLUS_3            0              9
  CLUS_4            0              3
  CLUS_5            2              6
  CLUS_6            1              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRF8 MUTATED        3      0      1      1
  IRF8 WILD-TYPE     19     11      6      7
D34V6, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            3             19
  CLUS_2            0             11
  CLUS_3            1              6
  CLUS_4            1              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF8 MUTATED        2      2      1
  IRF8 WILD-TYPE     14     14     14
D34V7, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            2             14
  CLUS_3            1             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IRF8 MUTATED        1      3      1      0      0
  IRF8 WILD-TYPE      8      9      7     12      6
D34V8, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            3              9
  CLUS_3            1              7
  CLUS_4            0             12
  CLUS_5            0              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRF8 MUTATED        1      0      0      2
  IRF8 WILD-TYPE      8     10      9     12
D34V9, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            0             10
  CLUS_3            0              9
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRF8 MUTATED        0      1      0      2
  IRF8 WILD-TYPE      8     14      5     12
D34V10, multiclass
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1             14
  CLUS_3            0              5
  CLUS_4            2             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = TMEM30A MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM30A MUTATED        4      0      0
  TMEM30A WILD-TYPE     16      7     21
D35V1, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               4                16
  CLUS_2               0                 7
  CLUS_3               0                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 CLUS_4
  TMEM30A MUTATED        1      1      1      1
  TMEM30A WILD-TYPE      8     12     18      6
D35V2, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                12
  CLUS_3               1                18
  CLUS_4               1                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TMEM30A MUTATED        0      0      0      1      2      0
  TMEM30A WILD-TYPE      6      5      5      5      4      5
D35V3, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               0                 5
  CLUS_3               0                 5
  CLUS_4               1                 5
  CLUS_5               2                 4
  CLUS_6               0                 5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM30A MUTATED        0      3      0
  TMEM30A WILD-TYPE      6     12     12
D35V4, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               0                 6
  CLUS_2               3                12
  CLUS_3               0                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TMEM30A MUTATED        1      2      0      0      0      1
  TMEM30A WILD-TYPE      9     10      9      3      8      5
D35V5, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               1                 9
  CLUS_2               2                10
  CLUS_3               0                 9
  CLUS_4               0                 3
  CLUS_5               0                 8
  CLUS_6               1                 5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM30A MUTATED        2      1      0      1
  TMEM30A WILD-TYPE     20     10      7      7
D35V6, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                10
  CLUS_3               0                 7
  CLUS_4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMEM30A MUTATED        1      1      2
  TMEM30A WILD-TYPE     15     15     13
D35V7, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                15
  CLUS_3               2                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 CLUS_4 CLUS_5
  TMEM30A MUTATED        2      2      0      0      0
  TMEM30A WILD-TYPE      7     10      8     12      6
D35V8, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                10
  CLUS_3               0                 8
  CLUS_4               0                12
  CLUS_5               0                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM30A MUTATED        1      1      0      1
  TMEM30A WILD-TYPE      8      9      9     13
D35V9, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 9
  CLUS_3               0                 9
  CLUS_4               1                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMEM30A MUTATED        0      1      0      2
  TMEM30A WILD-TYPE      8     14      5     12
D35V10, multiclass
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               1                14
  CLUS_3               0                 5
  CLUS_4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = UBE2A MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  UBE2A MUTATED        3      0      1
  UBE2A WILD-TYPE     17      7     20
D36V1, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             3              17
  CLUS_2             0               7
  CLUS_3             1              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 CLUS_4
  UBE2A MUTATED        1      0      3      0
  UBE2A WILD-TYPE      8     13     16      7
D36V2, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             1               8
  CLUS_2             0              13
  CLUS_3             3              16
  CLUS_4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  UBE2A MUTATED        1      0      1      0      1      0
  UBE2A WILD-TYPE      5      5      4      6      5      5
D36V3, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             1               5
  CLUS_2             0               5
  CLUS_3             1               4
  CLUS_4             0               6
  CLUS_5             1               5
  CLUS_6             0               5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  UBE2A MUTATED        0      2      1
  UBE2A WILD-TYPE      6     13     11
D36V4, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             0               6
  CLUS_2             2              13
  CLUS_3             1              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 CLUS_5 CLUS_6
  UBE2A MUTATED        1      0      1      0      2      0
  UBE2A WILD-TYPE      9     12      8      3      6      6
D36V5, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             1               9
  CLUS_2             0              12
  CLUS_3             1               8
  CLUS_4             0               3
  CLUS_5             2               6
  CLUS_6             0               6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UBE2A MUTATED        4      0      0      0
  UBE2A WILD-TYPE     18     11      7      8
D36V6, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             4              18
  CLUS_2             0              11
  CLUS_3             0               7
  CLUS_4             0               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  UBE2A MUTATED        2      2      0
  UBE2A WILD-TYPE     14     14     15
D36V7, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             2              14
  CLUS_2             2              14
  CLUS_3             0              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 CLUS_4 CLUS_5
  UBE2A MUTATED        0      0      2      0      2
  UBE2A WILD-TYPE      9     12      6     12      4
D36V8, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              12
  CLUS_3             2               6
  CLUS_4             0              12
  CLUS_5             2               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UBE2A MUTATED        2      0      0      2
  UBE2A WILD-TYPE      7     10      9     12
D36V9, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             2               7
  CLUS_2             0              10
  CLUS_3             0               9
  CLUS_4             2              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UBE2A MUTATED        2      1      0      1
  UBE2A WILD-TYPE      6     14      5     13
D36V10, multiclass
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  CLUS_1             2               6
  CLUS_2             1              14
  CLUS_3             0               5
  CLUS_4             1              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
