[1] "ofn"        "-oTLUSC-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/LUSC-TP/20140646/LUSC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/19940360/transformed.cor.cli.txt"

nPatients in clinical file=504, in cluster file=178, common to both=178
[1]  19 178
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           145             33 
  TP53 MUTATED TP53 WILD-TYPE 
           145             33 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              26              152 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              27              151 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            36            142 
  MLL2 MUTATED MLL2 WILD-TYPE 
            36            142 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             22             156 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
  PTEN MUTATED PTEN WILD-TYPE 
            14            164 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              151 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
  RB1 MUTATED RB1 WILD-TYPE 
           12           166 
[1] "CYP11B1 MUTATION ANALYSIS"
[1] 3
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
               15               163 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              14              164 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
  ASB5 MUTATED ASB5 WILD-TYPE 
             9            169 
[1] "IRF6 MUTATION ANALYSIS"
[1] 3
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            172 
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            172 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
  EP300 MUTATED EP300 WILD-TYPE 
              8             170 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            24            154 
  CPS1 MUTATED CPS1 WILD-TYPE 
            24            154 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              165 
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              165 
[1] "SLC28A1 MUTATION ANALYSIS"
[1] 3
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
  SLC28A1 MUTATED SLC28A1 WILD-TYPE 
                9               169 
[1] "POLR2B MUTATION ANALYSIS"
[1] 3
  POLR2B MUTATED POLR2B WILD-TYPE 
               6              172 
  POLR2B MUTATED POLR2B WILD-TYPE 
               6              172 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             5            173 
  HRAS MUTATED HRAS WILD-TYPE 
             5            173 
[1] "PI16 MUTATION ANALYSIS"
[1] 3
  PI16 MUTATED PI16 WILD-TYPE 
             7            171 
  PI16 MUTATED PI16 WILD-TYPE 
             7            171 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 178 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 178 columns, 0 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       29     44     11     15
  TP53 WILD-TYPE      8      4      6      4
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           29              8
  CLUS_2           44              4
  CLUS_3           11              6
  CLUS_4           15              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
  TP53 MUTATED       31     48     20
  TP53 WILD-TYPE     10      4      8
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           31             10
  CLUS_2           48              4
  CLUS_3           20              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       37     65     43
  TP53 WILD-TYPE     21      4      8
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           37             21
  CLUS_2           65              4
  CLUS_3           43              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       17     29     15
  TP53 WILD-TYPE     10      1      2
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           17             10
  CLUS_2           29              1
  CLUS_3           15              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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       24     34     27      4
  TP53 WILD-TYPE      8     11      2      2
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           24              8
  CLUS_2           34             11
  CLUS_3           27              2
  CLUS_4            4              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- 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       17     16     19     23     10      4
  TP53 WILD-TYPE      5      4      5      3      4      2
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           17              5
  CLUS_2           16              4
  CLUS_3           19              5
  CLUS_4           23              3
  CLUS_5           10              4
  CLUS_6            4              2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       31     56     44     14
  TP53 WILD-TYPE      9      6      6     12
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           31              9
  CLUS_2           56              6
  CLUS_3           44              6
  CLUS_4           14             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
  TP53 MUTATED       47     67     31
  TP53 WILD-TYPE     21      7      5
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           47             21
  CLUS_2           67              7
  CLUS_3           31              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       81     13     14     21      8
  TP53 WILD-TYPE     12      1      7      3      2
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           81             12
  CLUS_2           13              1
  CLUS_3           14              7
  CLUS_4           21              3
  CLUS_5            8              2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger 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       32     41     47     17
  TP53 WILD-TYPE      3     10      7      5
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           32              3
  CLUS_2           41             10
  CLUS_3           47              7
  CLUS_4           17              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
  TP53 MUTATED       10     18     12
  TP53 WILD-TYPE      6      1      1
D1V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              6
  CLUS_2           18              1
  CLUS_3           12              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4     19     17
  TP53 WILD-TYPE      0      0      8
D1V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4              0
  CLUS_2           19              0
  CLUS_3           17              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = CDKN2A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        0     13      3      2
  CDKN2A WILD-TYPE     37     35     14     17
D2V1, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              0               37
  CLUS_2             13               35
  CLUS_3              3               14
  CLUS_4              2               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        1     13      4
  CDKN2A WILD-TYPE     40     39     24
D2V2, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1               40
  CLUS_2             13               39
  CLUS_3              4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        3     15      8
  CDKN2A WILD-TYPE     55     54     43
D2V3, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              3               55
  CLUS_2             15               54
  CLUS_3              8               43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        2      4      3
  CDKN2A WILD-TYPE     25     26     14
D2V4, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               25
  CLUS_2              4               26
  CLUS_3              3               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
  CDKN2A MUTATED        2      8      3      0
  CDKN2A WILD-TYPE     30     37     26      6
D2V5, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               30
  CLUS_2              8               37
  CLUS_3              3               26
  CLUS_4              0                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CDKN2A MUTATED        2      2      4      1      2      2
  CDKN2A WILD-TYPE     20     18     20     25     12      4
D2V6, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              2               20
  CLUS_2              2               18
  CLUS_3              4               20
  CLUS_4              1               25
  CLUS_5              2               12
  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
  CDKN2A MUTATED        4     12      5      5
  CDKN2A WILD-TYPE     36     50     45     21
D2V7, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              4               36
  CLUS_2             12               50
  CLUS_3              5               45
  CLUS_4              5               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        6     16      4
  CDKN2A WILD-TYPE     62     58     32
D2V8, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              6               62
  CLUS_2             16               58
  CLUS_3              4               32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN2A MUTATED       16      1      4      3      0
  CDKN2A WILD-TYPE     77     13     17     21     10
D2V9, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1             16               77
  CLUS_2              1               13
  CLUS_3              4               17
  CLUS_4              3               21
  CLUS_5              0               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN2A MUTATED        5      6     10      3
  CDKN2A WILD-TYPE     30     45     44     19
D2V10, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              5               30
  CLUS_2              6               45
  CLUS_3             10               44
  CLUS_4              3               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN2A MUTATED        1      2      2
  CDKN2A WILD-TYPE     15     17     11
D2V11, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1               15
  CLUS_2              2               17
  CLUS_3              2               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
  CDKN2A MUTATED        1      4      0
  CDKN2A WILD-TYPE      3     15     25
D2V12, multiclass
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  CLUS_1              1                3
  CLUS_2              4               15
  CLUS_3              0               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = NFE2L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFE2L2 MUTATED        0     14      1      1
  NFE2L2 WILD-TYPE     37     34     16     18
D3V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               37
  CLUS_2             14               34
  CLUS_3              1               16
  CLUS_4              1               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        0     14      2
  NFE2L2 WILD-TYPE     41     38     26
D3V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0               41
  CLUS_2             14               38
  CLUS_3              2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        7     17      3
  NFE2L2 WILD-TYPE     51     52     48
D3V3, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              7               51
  CLUS_2             17               52
  CLUS_3              3               48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        4      8      0
  NFE2L2 WILD-TYPE     23     22     17
D3V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               23
  CLUS_2              8               22
  CLUS_3              0               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
  NFE2L2 MUTATED        8      4      7      0
  NFE2L2 WILD-TYPE     24     41     22      6
D3V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              8               24
  CLUS_2              4               41
  CLUS_3              7               22
  CLUS_4              0                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NFE2L2 MUTATED        4      3      1      7      3      1
  NFE2L2 WILD-TYPE     18     17     23     19     11      5
D3V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               18
  CLUS_2              3               17
  CLUS_3              1               23
  CLUS_4              7               19
  CLUS_5              3               11
  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
  NFE2L2 MUTATED        2     22      1      2
  NFE2L2 WILD-TYPE     38     40     49     24
D3V7, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               38
  CLUS_2             22               40
  CLUS_3              1               49
  CLUS_4              2               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        2     24      1
  NFE2L2 WILD-TYPE     66     50     35
D3V8, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               66
  CLUS_2             24               50
  CLUS_3              1               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NFE2L2 MUTATED       14      1      1     10      0
  NFE2L2 WILD-TYPE     79     13     20     14     10
D3V9, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1             14               79
  CLUS_2              1               13
  CLUS_3              1               20
  CLUS_4             10               14
  CLUS_5              0               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFE2L2 MUTATED       15      6      2      3
  NFE2L2 WILD-TYPE     20     45     52     19
D3V10, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1             15               20
  CLUS_2              6               45
  CLUS_3              2               52
  CLUS_4              3               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NFE2L2 MUTATED        3      2      3
  NFE2L2 WILD-TYPE     13     17     10
D3V11, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              3               13
  CLUS_2              2               17
  CLUS_3              3               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
  NFE2L2 MUTATED        0      4      4
  NFE2L2 WILD-TYPE      4     15     21
D3V12, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              4               15
  CLUS_3              4               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"

Clustering(4) Variable = MLL2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        4     10      6      5
  MLL2 WILD-TYPE     33     38     11     14
D4V1, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             33
  CLUS_2           10             38
  CLUS_3            6             11
  CLUS_4            5             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
  MLL2 MUTATED        6     13      6
  MLL2 WILD-TYPE     35     39     22
D4V2, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             35
  CLUS_2           13             39
  CLUS_3            6             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        9     15     12
  MLL2 WILD-TYPE     49     54     39
D4V3, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            9             49
  CLUS_2           15             54
  CLUS_3           12             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MLL2 MUTATED        6      7      1
  MLL2 WILD-TYPE     21     23     16
D4V4, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            6             21
  CLUS_2            7             23
  CLUS_3            1             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
  MLL2 MUTATED        7      9      7      1
  MLL2 WILD-TYPE     25     36     22      5
D4V5, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            7             25
  CLUS_2            9             36
  CLUS_3            7             22
  CLUS_4            1              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MLL2 MUTATED        5      4      6      5      2      2
  MLL2 WILD-TYPE     17     16     18     21     12      4
D4V6, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             17
  CLUS_2            4             16
  CLUS_3            6             18
  CLUS_4            5             21
  CLUS_5            2             12
  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
  MLL2 MUTATED        5     15     11      5
  MLL2 WILD-TYPE     35     47     39     21
D4V7, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             35
  CLUS_2           15             47
  CLUS_3           11             39
  CLUS_4            5             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       12     17      7
  MLL2 WILD-TYPE     56     57     29
D4V8, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           12             56
  CLUS_2           17             57
  CLUS_3            7             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MLL2 MUTATED       17      2      5      4      2
  MLL2 WILD-TYPE     76     12     16     20      8
D4V9, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1           17             76
  CLUS_2            2             12
  CLUS_3            5             16
  CLUS_4            4             20
  CLUS_5            2              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MLL2 MUTATED        5     10     11      4
  MLL2 WILD-TYPE     30     41     43     18
D4V10, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            5             30
  CLUS_2           10             41
  CLUS_3           11             43
  CLUS_4            4             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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      3      3
  MLL2 WILD-TYPE     12     16     10
D4V11, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            4             12
  CLUS_2            3             16
  CLUS_3            3             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
  MLL2 MUTATED        1      4      5
  MLL2 WILD-TYPE      3     15     20
D4V12, multiclass
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  CLUS_1            1              3
  CLUS_2            4             15
  CLUS_3            5             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"

Clustering(5) Variable = KEAP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        0     12      1      4
  KEAP1 WILD-TYPE     37     36     16     15
D5V1, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              37
  CLUS_2            12              36
  CLUS_3             1              16
  CLUS_4             4              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        0     13      4
  KEAP1 WILD-TYPE     41     39     24
D5V2, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              41
  CLUS_2            13              39
  CLUS_3             4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        4     13      5
  KEAP1 WILD-TYPE     54     56     46
D5V3, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             4              54
  CLUS_2            13              56
  CLUS_3             5              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        0      4      3
  KEAP1 WILD-TYPE     27     26     14
D5V4, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              27
  CLUS_2             4              26
  CLUS_3             3              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
  KEAP1 MUTATED        1      2      7      1
  KEAP1 WILD-TYPE     31     43     22      5
D5V5, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             1              31
  CLUS_2             2              43
  CLUS_3             7              22
  CLUS_4             1               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KEAP1 MUTATED        2      4      1      4      0      0
  KEAP1 WILD-TYPE     20     16     23     22     14      6
D5V6, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             4              16
  CLUS_3             1              23
  CLUS_4             4              22
  CLUS_5             0              14
  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
  KEAP1 MUTATED        2     12      5      3
  KEAP1 WILD-TYPE     38     50     45     23
D5V7, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             2              38
  CLUS_2            12              50
  CLUS_3             5              45
  CLUS_4             3              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        3     13      6
  KEAP1 WILD-TYPE     65     61     30
D5V8, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             3              65
  CLUS_2            13              61
  CLUS_3             6              30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KEAP1 MUTATED       10      3      0      3      2
  KEAP1 WILD-TYPE     83     11     21     21      8
D5V9, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1            10              83
  CLUS_2             3              11
  CLUS_3             0              21
  CLUS_4             3              21
  CLUS_5             2               8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KEAP1 MUTATED        5      3      8      2
  KEAP1 WILD-TYPE     30     48     46     20
D5V10, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             5              30
  CLUS_2             3              48
  CLUS_3             8              46
  CLUS_4             2              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KEAP1 MUTATED        0      2      1
  KEAP1 WILD-TYPE     16     17     12
D5V11, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0              16
  CLUS_2             2              17
  CLUS_3             1              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
  KEAP1 MUTATED        0      2      1
  KEAP1 WILD-TYPE      4     17     24
D5V12, multiclass
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             2              17
  CLUS_3             1              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        4      2      0      2
  PTEN WILD-TYPE     33     46     17     17
D6V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             33
  CLUS_2            2             46
  CLUS_3            0             17
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        5      2      1
  PTEN WILD-TYPE     36     50     27
D6V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             36
  CLUS_2            2             50
  CLUS_3            1             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        7      4      3
  PTEN WILD-TYPE     51     65     48
D6V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             51
  CLUS_2            4             65
  CLUS_3            3             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        5      3      0
  PTEN WILD-TYPE     22     27     17
D6V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             22
  CLUS_2            3             27
  CLUS_3            0             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
  PTEN MUTATED        2      4      2      0
  PTEN WILD-TYPE     30     41     27      6
D6V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             30
  CLUS_2            4             41
  CLUS_3            2             27
  CLUS_4            0              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTEN MUTATED        1      1      1      3      2      0
  PTEN WILD-TYPE     21     19     23     23     12      6
D6V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             21
  CLUS_2            1             19
  CLUS_3            1             23
  CLUS_4            3             23
  CLUS_5            2             12
  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
  PTEN MUTATED        4      3      4      3
  PTEN WILD-TYPE     36     59     46     23
D6V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             36
  CLUS_2            3             59
  CLUS_3            4             46
  CLUS_4            3             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        6      4      4
  PTEN WILD-TYPE     62     70     32
D6V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             62
  CLUS_2            4             70
  CLUS_3            4             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        7      0      3      1      1
  PTEN WILD-TYPE     86     14     18     23      9
D6V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             86
  CLUS_2            0             14
  CLUS_3            3             18
  CLUS_4            1             23
  CLUS_5            1              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        1      3      6      2
  PTEN WILD-TYPE     34     48     48     20
D6V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             34
  CLUS_2            3             48
  CLUS_3            6             48
  CLUS_4            2             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      4      0
  PTEN WILD-TYPE     15     15     13
D6V11, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             15
  CLUS_2            4             15
  CLUS_3            0             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
  PTEN MUTATED        0      2      3
  PTEN WILD-TYPE      4     17     22
D6V12, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              4
  CLUS_2            2             17
  CLUS_3            3             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        4      6      3      4
  PIK3CA WILD-TYPE     33     42     14     15
D7V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               33
  CLUS_2              6               42
  CLUS_3              3               14
  CLUS_4              4               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        7      6      4
  PIK3CA WILD-TYPE     34     46     24
D7V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               34
  CLUS_2              6               46
  CLUS_3              4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       10      7     10
  PIK3CA WILD-TYPE     48     62     41
D7V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             10               48
  CLUS_2              7               62
  CLUS_3             10               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        4      4      3
  PIK3CA WILD-TYPE     23     26     14
D7V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               23
  CLUS_2              4               26
  CLUS_3              3               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
  PIK3CA MUTATED        6      7      4      0
  PIK3CA WILD-TYPE     26     38     25      6
D7V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               26
  CLUS_2              7               38
  CLUS_3              4               25
  CLUS_4              0                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PIK3CA MUTATED        3      5      4      4      1      0
  PIK3CA WILD-TYPE     19     15     20     22     13      6
D7V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               19
  CLUS_2              5               15
  CLUS_3              4               20
  CLUS_4              4               22
  CLUS_5              1               13
  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
  PIK3CA MUTATED        8      7     10      2
  PIK3CA WILD-TYPE     32     55     40     24
D7V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               32
  CLUS_2              7               55
  CLUS_3             10               40
  CLUS_4              2               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       11      9      7
  PIK3CA WILD-TYPE     57     65     29
D7V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               57
  CLUS_2              9               65
  CLUS_3              7               29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED       15      4      3      2      0
  PIK3CA WILD-TYPE     78     10     18     22     10
D7V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             15               78
  CLUS_2              4               10
  CLUS_3              3               18
  CLUS_4              2               22
  CLUS_5              0               10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        3     11      8      2
  PIK3CA WILD-TYPE     32     40     46     20
D7V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               32
  CLUS_2             11               40
  CLUS_3              8               46
  CLUS_4              2               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        2      4      3
  PIK3CA WILD-TYPE     14     15     10
D7V11, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               14
  CLUS_2              4               15
  CLUS_3              3               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
  PIK3CA MUTATED        1      4      4
  PIK3CA WILD-TYPE      3     15     21
D7V12, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                3
  CLUS_2              4               15
  CLUS_3              4               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"

Clustering(8) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        2      5      0      3
  RB1 WILD-TYPE     35     43     17     16
D8V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            35
  CLUS_2           5            43
  CLUS_3           0            17
  CLUS_4           3            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      5      3
  RB1 WILD-TYPE     39     47     25
D8V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            39
  CLUS_2           5            47
  CLUS_3           3            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        4      3      5
  RB1 WILD-TYPE     54     66     46
D8V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           4            54
  CLUS_2           3            66
  CLUS_3           5            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        0      4      1
  RB1 WILD-TYPE     27     26     16
D8V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            27
  CLUS_2           4            26
  CLUS_3           1            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
  RB1 MUTATED        0      2      3      1
  RB1 WILD-TYPE     32     43     26      5
D8V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            32
  CLUS_2           2            43
  CLUS_3           3            26
  CLUS_4           1             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RB1 MUTATED        0      1      2      3      0      0
  RB1 WILD-TYPE     22     19     22     23     14      6
D8V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            22
  CLUS_2           1            19
  CLUS_3           2            22
  CLUS_4           3            23
  CLUS_5           0            14
  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
  RB1 MUTATED        2      4      3      3
  RB1 WILD-TYPE     38     58     47     23
D8V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            38
  CLUS_2           4            58
  CLUS_3           3            47
  CLUS_4           3            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        2      6      4
  RB1 WILD-TYPE     66     68     32
D8V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            66
  CLUS_2           6            68
  CLUS_3           4            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RB1 MUTATED        7      1      0      2      2
  RB1 WILD-TYPE     86     13     21     22      8
D8V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           7            86
  CLUS_2           1            13
  CLUS_3           0            21
  CLUS_4           2            22
  CLUS_5           2             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        2      3      6      1
  RB1 WILD-TYPE     33     48     48     21
D8V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            33
  CLUS_2           3            48
  CLUS_3           6            48
  CLUS_4           1            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        0      1      0
  RB1 WILD-TYPE     16     18     13
D8V11, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            47 
   TCGA-21-5782    TCGA-21-5784    TCGA-21-5786    TCGA-22-5471    TCGA-22-5472 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5473    TCGA-22-5474    TCGA-22-5477    TCGA-22-5478    TCGA-22-5480 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5482    TCGA-22-5485    TCGA-22-5489    TCGA-22-5491    TCGA-22-5492 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-33-6737    TCGA-34-5231    TCGA-34-5232    TCGA-34-5234    TCGA-34-5236 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-34-5239    TCGA-34-5927    TCGA-34-5928    TCGA-34-5929    TCGA-37-3783 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-37-5819    TCGA-39-5019    TCGA-39-5022    TCGA-39-5024    TCGA-39-5027 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-43-5668    TCGA-43-6647    TCGA-43-6770    TCGA-43-6771    TCGA-46-6025 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-46-6026    TCGA-56-5897    TCGA-56-5898    TCGA-56-6545    TCGA-56-6546 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-60-2709    TCGA-63-6202    TCGA-70-6722    TCGA-70-6723    TCGA-85-6175 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-85-6560    TCGA-85-6561 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        0      1      0
  RB1 WILD-TYPE      4     18     25
D8V12, multiclass
[1] "Remove cluster labels:" "RB1 MUTATED"           
clus
  RB1 MUTATED RB1 WILD-TYPE 
            1            47 
   TCGA-21-5782    TCGA-21-5784    TCGA-21-5786    TCGA-22-5471    TCGA-22-5472 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5473    TCGA-22-5474    TCGA-22-5477    TCGA-22-5478    TCGA-22-5480 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-22-5482    TCGA-22-5485    TCGA-22-5489    TCGA-22-5491    TCGA-22-5492 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-33-6737    TCGA-34-5231    TCGA-34-5232    TCGA-34-5234    TCGA-34-5236 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-34-5239    TCGA-34-5927    TCGA-34-5928    TCGA-34-5929    TCGA-37-3783 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-37-5819    TCGA-39-5019    TCGA-39-5022    TCGA-39-5024    TCGA-39-5027 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-43-5668    TCGA-43-6647    TCGA-43-6770    TCGA-43-6771    TCGA-46-6025 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-46-6026    TCGA-56-5897    TCGA-56-5898    TCGA-56-6545    TCGA-56-6546 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-60-2709    TCGA-63-6202    TCGA-70-6722    TCGA-70-6723    TCGA-85-6175 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" "RB1 WILD-TYPE" 
   TCGA-85-6560    TCGA-85-6561 
"RB1 WILD-TYPE" "RB1 WILD-TYPE" 

Clustering(9) Variable = CYP11B1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        3      5      3      1
  CYP11B1 WILD-TYPE     34     43     14     18
D9V1, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                34
  CLUS_2               5                43
  CLUS_3               3                14
  CLUS_4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        3      5      4
  CYP11B1 WILD-TYPE     38     47     24
D9V2, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                38
  CLUS_2               5                47
  CLUS_3               4                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        4      5      6
  CYP11B1 WILD-TYPE     54     64     45
D9V3, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               4                54
  CLUS_2               5                64
  CLUS_3               6                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        3      1      0
  CYP11B1 WILD-TYPE     24     29     17
D9V4, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                24
  CLUS_2               1                29
  CLUS_3               0                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
  CYP11B1 MUTATED        2      3      4      0
  CYP11B1 WILD-TYPE     30     42     25      6
D9V5, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                30
  CLUS_2               3                42
  CLUS_3               4                25
  CLUS_4               0                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CYP11B1 MUTATED        2      4      1      2      0      0
  CYP11B1 WILD-TYPE     20     16     23     24     14      6
D9V6, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                20
  CLUS_2               4                16
  CLUS_3               1                23
  CLUS_4               2                24
  CLUS_5               0                14
  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
  CYP11B1 MUTATED        2      4      6      3
  CYP11B1 WILD-TYPE     38     58     44     23
D9V7, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               2                38
  CLUS_2               4                58
  CLUS_3               6                44
  CLUS_4               3                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        4      6      5
  CYP11B1 WILD-TYPE     64     68     31
D9V8, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               4                64
  CLUS_2               6                68
  CLUS_3               5                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CYP11B1 MUTATED        6      2      1      3      1
  CYP11B1 WILD-TYPE     87     12     20     21      9
D9V9, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               6                87
  CLUS_2               2                12
  CLUS_3               1                20
  CLUS_4               3                21
  CLUS_5               1                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CYP11B1 MUTATED        3      4      5      1
  CYP11B1 WILD-TYPE     32     47     49     21
D9V10, multiclass
        clus
vv       CYP11B1 MUTATED CYP11B1 WILD-TYPE
  CLUS_1               3                32
  CLUS_2               4                47
  CLUS_3               5                49
  CLUS_4               1                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        1      0      1
  CYP11B1 WILD-TYPE     15     19     12
D9V11, multiclass
[1] "Remove cluster labels:" "CYP11B1 MUTATED"       
clus
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                2                46 
       TCGA-21-5782        TCGA-21-5784        TCGA-21-5786        TCGA-22-5471 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-22-5472        TCGA-22-5473        TCGA-22-5474        TCGA-22-5477 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-22-5478        TCGA-22-5480        TCGA-22-5482        TCGA-22-5485 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-22-5489        TCGA-22-5492        TCGA-33-6737        TCGA-34-5231 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-34-5232        TCGA-34-5234        TCGA-34-5236        TCGA-34-5239 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-34-5927        TCGA-34-5928        TCGA-34-5929        TCGA-37-3783 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-37-5819        TCGA-39-5019        TCGA-39-5022        TCGA-39-5024 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-39-5027        TCGA-43-5668        TCGA-43-6143        TCGA-43-6647 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-43-6770        TCGA-46-6025        TCGA-46-6026        TCGA-56-5897 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-56-5898        TCGA-56-6545        TCGA-56-6546        TCGA-60-2709 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-63-6202        TCGA-70-6722        TCGA-70-6723        TCGA-85-6175 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-85-6560        TCGA-85-6561 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CYP11B1 MUTATED        0      1      1
  CYP11B1 WILD-TYPE      4     18     24
D9V12, multiclass
[1] "Remove cluster labels:" "CYP11B1 MUTATED"       
clus
  CYP11B1 MUTATED CYP11B1 WILD-TYPE 
                2                46 
       TCGA-21-5782        TCGA-21-5784        TCGA-21-5786        TCGA-22-5471 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-22-5472        TCGA-22-5473        TCGA-22-5474        TCGA-22-5477 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-22-5478        TCGA-22-5480        TCGA-22-5482        TCGA-22-5485 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-22-5489        TCGA-22-5492        TCGA-33-6737        TCGA-34-5231 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-34-5232        TCGA-34-5234        TCGA-34-5236        TCGA-34-5239 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-34-5927        TCGA-34-5928        TCGA-34-5929        TCGA-37-3783 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-37-5819        TCGA-39-5019        TCGA-39-5022        TCGA-39-5024 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-39-5027        TCGA-43-5668        TCGA-43-6143        TCGA-43-6647 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-43-6770        TCGA-46-6025        TCGA-46-6026        TCGA-56-5897 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-56-5898        TCGA-56-6545        TCGA-56-6546        TCGA-60-2709 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-63-6202        TCGA-70-6722        TCGA-70-6723        TCGA-85-6175 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 
       TCGA-85-6560        TCGA-85-6561 
"CYP11B1 WILD-TYPE" "CYP11B1 WILD-TYPE" 

Clustering(10) Variable = NOTCH1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH1 MUTATED        1      4      1      1
  NOTCH1 WILD-TYPE     36     44     16     18
D10V1, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               36
  CLUS_2              4               44
  CLUS_3              1               16
  CLUS_4              1               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        1      4      2
  NOTCH1 WILD-TYPE     40     48     26
D10V2, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               40
  CLUS_2              4               48
  CLUS_3              2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        3      5      6
  NOTCH1 WILD-TYPE     55     64     45
D10V3, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               55
  CLUS_2              5               64
  CLUS_3              6               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        0      5      3
  NOTCH1 WILD-TYPE     27     25     14
D10V4, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0               27
  CLUS_2              5               25
  CLUS_3              3               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
  NOTCH1 MUTATED        3      3      1      1
  NOTCH1 WILD-TYPE     29     42     28      5
D10V5, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               29
  CLUS_2              3               42
  CLUS_3              1               28
  CLUS_4              1                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NOTCH1 MUTATED        1      2      1      4      0      0
  NOTCH1 WILD-TYPE     21     18     23     22     14      6
D10V6, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               21
  CLUS_2              2               18
  CLUS_3              1               23
  CLUS_4              4               22
  CLUS_5              0               14
  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
  NOTCH1 MUTATED        2      6      5      1
  NOTCH1 WILD-TYPE     38     56     45     25
D10V7, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2               38
  CLUS_2              6               56
  CLUS_3              5               45
  CLUS_4              1               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        3      8      3
  NOTCH1 WILD-TYPE     65     66     33
D10V8, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               65
  CLUS_2              8               66
  CLUS_3              3               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NOTCH1 MUTATED        7      2      0      3      1
  NOTCH1 WILD-TYPE     86     12     21     21      9
D10V9, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              7               86
  CLUS_2              2               12
  CLUS_3              0               21
  CLUS_4              3               21
  CLUS_5              1                9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NOTCH1 MUTATED        4      3      6      0
  NOTCH1 WILD-TYPE     31     48     48     22
D10V10, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              4               31
  CLUS_2              3               48
  CLUS_3              6               48
  CLUS_4              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NOTCH1 MUTATED        1      0      4
  NOTCH1 WILD-TYPE     15     19      9
D10V11, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               15
  CLUS_2              0               19
  CLUS_3              4                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
  NOTCH1 MUTATED        1      4      0
  NOTCH1 WILD-TYPE      3     15     25
D10V12, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1                3
  CLUS_2              4               15
  CLUS_3              0               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = ASB5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASB5 MUTATED        1      4      2      2
  ASB5 WILD-TYPE     36     44     15     17
D11V1, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            1             36
  CLUS_2            4             44
  CLUS_3            2             15
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        2      4      3
  ASB5 WILD-TYPE     39     48     25
D11V2, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            2             39
  CLUS_2            4             48
  CLUS_3            3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        2      6      1
  ASB5 WILD-TYPE     56     63     50
D11V3, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            2             56
  CLUS_2            6             63
  CLUS_3            1             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        0      2      0
  ASB5 WILD-TYPE     27     28     17
D11V4, multiclass
[1] "Remove cluster labels:" "ASB5 MUTATED"          
clus
  ASB5 MUTATED ASB5 WILD-TYPE 
             2             72 
    TCGA-18-3417     TCGA-18-4721     TCGA-18-5592     TCGA-18-5595 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-21-5787 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-4593     TCGA-22-4599     TCGA-22-4601     TCGA-22-5471 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-4566 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-33-4582     TCGA-33-4583     TCGA-33-4586     TCGA-33-6737 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5231     TCGA-34-5232     TCGA-34-5234     TCGA-34-5236 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5239     TCGA-34-5240     TCGA-34-5241     TCGA-34-5927 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-34-5928     TCGA-34-5929     TCGA-37-5819     TCGA-39-5019 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-39-5021     TCGA-39-5022     TCGA-39-5024     TCGA-39-5027 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-39-5028     TCGA-39-5029     TCGA-39-5030     TCGA-39-5031 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-39-5035     TCGA-39-5036     TCGA-39-5037     TCGA-39-5039 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-43-5668     TCGA-43-6143     TCGA-43-6647     TCGA-43-6770 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-43-6771     TCGA-46-6025     TCGA-46-6026     TCGA-56-5897 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-56-5898     TCGA-56-6545     TCGA-56-6546     TCGA-60-2709 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-63-5128     TCGA-63-5131     TCGA-63-6202     TCGA-70-6722 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-70-6723     TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASB5 MUTATED        0      1      2      0
  ASB5 WILD-TYPE     32     44     27      6
D11V5, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            1             44
  CLUS_3            2             27
  CLUS_4            0              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ASB5 MUTATED        1      0      1      1      0      0
  ASB5 WILD-TYPE     21     20     23     25     14      6
D11V6, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            0             20
  CLUS_3            1             23
  CLUS_4            1             25
  CLUS_5            0             14
  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
  ASB5 MUTATED        1      4      4      0
  ASB5 WILD-TYPE     39     58     46     26
D11V7, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            1             39
  CLUS_2            4             58
  CLUS_3            4             46
  CLUS_4            0             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        2      4      3
  ASB5 WILD-TYPE     66     70     33
D11V8, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            2             66
  CLUS_2            4             70
  CLUS_3            3             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ASB5 MUTATED        5      2      0      0      0
  ASB5 WILD-TYPE     88     12     21     24     10
D11V9, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            5             88
  CLUS_2            2             12
  CLUS_3            0             21
  CLUS_4            0             24
  CLUS_5            0             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASB5 MUTATED        0      4      2      1
  ASB5 WILD-TYPE     35     47     52     21
D11V10, multiclass
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  CLUS_1            0             35
  CLUS_2            4             47
  CLUS_3            2             52
  CLUS_4            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        0      0      0
  ASB5 WILD-TYPE     16     19     13
D11V11, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ASB5 MUTATED        0      0      0
  ASB5 WILD-TYPE      4     19     25
D11V12, multiclass

Clustering(12) Variable = IRF6 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRF6 MUTATED        1      1      2      0
  IRF6 WILD-TYPE     36     47     15     19
D12V1, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            1             36
  CLUS_2            1             47
  CLUS_3            2             15
  CLUS_4            0             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF6 MUTATED        1      1      2
  IRF6 WILD-TYPE     40     51     26
D12V2, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            1             40
  CLUS_2            1             51
  CLUS_3            2             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF6 MUTATED        4      2      0
  IRF6 WILD-TYPE     54     67     51
D12V3, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            4             54
  CLUS_2            2             67
  CLUS_3            0             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF6 MUTATED        2      0      1
  IRF6 WILD-TYPE     25     30     16
D12V4, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            2             25
  CLUS_2            0             30
  CLUS_3            1             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
  IRF6 MUTATED        1      2      2      0
  IRF6 WILD-TYPE     31     43     27      6
D12V5, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            1             31
  CLUS_2            2             43
  CLUS_3            2             27
  CLUS_4            0              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  IRF6 MUTATED        0      3      1      0      1      0
  IRF6 WILD-TYPE     22     17     23     26     13      6
D12V6, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            0             22
  CLUS_2            3             17
  CLUS_3            1             23
  CLUS_4            0             26
  CLUS_5            1             13
  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
  IRF6 MUTATED        2      1      2      1
  IRF6 WILD-TYPE     38     61     48     25
D12V7, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            2             38
  CLUS_2            1             61
  CLUS_3            2             48
  CLUS_4            1             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF6 MUTATED        2      2      2
  IRF6 WILD-TYPE     66     72     34
D12V8, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            2             66
  CLUS_2            2             72
  CLUS_3            2             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IRF6 MUTATED        2      1      0      1      0
  IRF6 WILD-TYPE     91     13     21     23     10
D12V9, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            2             91
  CLUS_2            1             13
  CLUS_3            0             21
  CLUS_4            1             23
  CLUS_5            0             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IRF6 MUTATED        1      1      1      1
  IRF6 WILD-TYPE     34     50     53     21
D12V10, multiclass
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  CLUS_1            1             34
  CLUS_2            1             50
  CLUS_3            1             53
  CLUS_4            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF6 MUTATED        0      1      0
  IRF6 WILD-TYPE     16     18     13
D12V11, multiclass
[1] "Remove cluster labels:" "IRF6 MUTATED"          
clus
  IRF6 MUTATED IRF6 WILD-TYPE 
             1             47 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-22-5471 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-6737 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-34-5232     TCGA-34-5234     TCGA-34-5236     TCGA-34-5239 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-34-5927     TCGA-34-5928     TCGA-34-5929     TCGA-37-3783 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-37-5819     TCGA-39-5019     TCGA-39-5022     TCGA-39-5024 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-39-5027     TCGA-43-5668     TCGA-43-6143     TCGA-43-6647 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-60-2709     TCGA-63-6202     TCGA-70-6722     TCGA-70-6723 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IRF6 MUTATED        0      1      0
  IRF6 WILD-TYPE      4     18     25
D12V12, multiclass
[1] "Remove cluster labels:" "IRF6 MUTATED"          
clus
  IRF6 MUTATED IRF6 WILD-TYPE 
             1             47 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-22-5471 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-6737 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-34-5232     TCGA-34-5234     TCGA-34-5236     TCGA-34-5239 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-34-5927     TCGA-34-5928     TCGA-34-5929     TCGA-37-3783 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-37-5819     TCGA-39-5019     TCGA-39-5022     TCGA-39-5024 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-39-5027     TCGA-43-5668     TCGA-43-6143     TCGA-43-6647 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-60-2709     TCGA-63-6202     TCGA-70-6722     TCGA-70-6723 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 
    TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"IRF6 WILD-TYPE" "IRF6 WILD-TYPE" "IRF6 WILD-TYPE" 

Clustering(13) Variable = EP300 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        5      2      0      0
  EP300 WILD-TYPE     32     46     17     19
D13V1, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              32
  CLUS_2             2              46
  CLUS_3             0              17
  CLUS_4             0              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        5      2      0
  EP300 WILD-TYPE     36     50     28
D13V2, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             5              36
  CLUS_2             2              50
  CLUS_3             0              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        2      2      4
  EP300 WILD-TYPE     56     67     47
D13V3, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             2              56
  CLUS_2             2              67
  CLUS_3             4              47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        0      1      0
  EP300 WILD-TYPE     27     29     17
D13V4, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              1              73 
     TCGA-18-3417      TCGA-18-4721      TCGA-18-5592      TCGA-18-5595 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-21-5782      TCGA-21-5784      TCGA-21-5787      TCGA-22-4593 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-4599      TCGA-22-4601      TCGA-22-4613      TCGA-22-5471 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5472      TCGA-22-5473      TCGA-22-5474      TCGA-22-5477 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5478      TCGA-22-5480      TCGA-22-5482      TCGA-22-5485 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5489      TCGA-22-5491      TCGA-22-5492      TCGA-33-4566 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-33-4582      TCGA-33-4583      TCGA-33-4586      TCGA-33-6737 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5231      TCGA-34-5232      TCGA-34-5234      TCGA-34-5236 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5239      TCGA-34-5240      TCGA-34-5241      TCGA-34-5927 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5928      TCGA-34-5929      TCGA-37-5819      TCGA-39-5016 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5021      TCGA-39-5022      TCGA-39-5024 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5027      TCGA-39-5028      TCGA-39-5029      TCGA-39-5030 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5031      TCGA-39-5035      TCGA-39-5036      TCGA-39-5037 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5039      TCGA-43-5668      TCGA-43-6143      TCGA-43-6647 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6770      TCGA-43-6771      TCGA-46-6025      TCGA-46-6026 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-56-5897      TCGA-56-5898      TCGA-56-6545      TCGA-56-6546 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-60-2709      TCGA-63-5128      TCGA-63-5131      TCGA-63-6202 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-70-6722      TCGA-70-6723      TCGA-85-6175      TCGA-85-6560 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6561 
"EP300 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        1      1      1      0
  EP300 WILD-TYPE     31     44     28      6
D13V5, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             1              31
  CLUS_2             1              44
  CLUS_3             1              28
  CLUS_4             0               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  EP300 MUTATED        0      0      1      2      0      0
  EP300 WILD-TYPE     22     20     23     24     14      6
D13V6, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             0              22
  CLUS_2             0              20
  CLUS_3             1              23
  CLUS_4             2              24
  CLUS_5             0              14
  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
  EP300 MUTATED        3      0      3      2
  EP300 WILD-TYPE     37     62     47     24
D13V7, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             3              37
  CLUS_2             0              62
  CLUS_3             3              47
  CLUS_4             2              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        6      1      1
  EP300 WILD-TYPE     62     73     35
D13V8, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             6              62
  CLUS_2             1              73
  CLUS_3             1              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EP300 MUTATED        6      1      0      0      0
  EP300 WILD-TYPE     87     13     21     24     10
D13V9, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             6              87
  CLUS_2             1              13
  CLUS_3             0              21
  CLUS_4             0              24
  CLUS_5             0              10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EP300 MUTATED        1      3      3      0
  EP300 WILD-TYPE     34     48     51     22
D13V10, multiclass
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  CLUS_1             1              34
  CLUS_2             3              48
  CLUS_3             3              51
  CLUS_4             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        1      1      0
  EP300 WILD-TYPE     15     18     13
D13V11, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              46 
     TCGA-21-5782      TCGA-21-5784      TCGA-22-5471      TCGA-22-5472 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5473      TCGA-22-5474      TCGA-22-5477      TCGA-22-5478 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5480      TCGA-22-5482      TCGA-22-5485      TCGA-22-5489 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5491      TCGA-22-5492      TCGA-33-6737      TCGA-34-5231 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5232      TCGA-34-5234      TCGA-34-5236      TCGA-34-5239 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5927      TCGA-34-5928      TCGA-34-5929      TCGA-37-5819 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5022      TCGA-39-5024      TCGA-39-5027 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-5668      TCGA-43-6143      TCGA-43-6647      TCGA-43-6770 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6771      TCGA-46-6025      TCGA-46-6026      TCGA-56-5897 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-56-5898      TCGA-56-6545      TCGA-56-6546      TCGA-60-2709 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-63-6202      TCGA-70-6722      TCGA-70-6723      TCGA-85-6175 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6560      TCGA-85-6561 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EP300 MUTATED        1      0      1
  EP300 WILD-TYPE      3     19     24
D13V12, multiclass
[1] "Remove cluster labels:" "EP300 MUTATED"         
clus
  EP300 MUTATED EP300 WILD-TYPE 
              2              46 
     TCGA-21-5782      TCGA-21-5784      TCGA-22-5471      TCGA-22-5472 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5473      TCGA-22-5474      TCGA-22-5477      TCGA-22-5478 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5480      TCGA-22-5482      TCGA-22-5485      TCGA-22-5489 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-22-5491      TCGA-22-5492      TCGA-33-6737      TCGA-34-5231 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5232      TCGA-34-5234      TCGA-34-5236      TCGA-34-5239 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-34-5927      TCGA-34-5928      TCGA-34-5929      TCGA-37-5819 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-39-5019      TCGA-39-5022      TCGA-39-5024      TCGA-39-5027 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-5668      TCGA-43-6143      TCGA-43-6647      TCGA-43-6770 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-43-6771      TCGA-46-6025      TCGA-46-6026      TCGA-56-5897 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-56-5898      TCGA-56-6545      TCGA-56-6546      TCGA-60-2709 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-63-6202      TCGA-70-6722      TCGA-70-6723      TCGA-85-6175 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" "EP300 WILD-TYPE" 
     TCGA-85-6560      TCGA-85-6561 
"EP300 WILD-TYPE" "EP300 WILD-TYPE" 

Clustering(14) Variable = CPS1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CPS1 MUTATED        5      7      4      2
  CPS1 WILD-TYPE     32     41     13     17
D14V1, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            5             32
  CLUS_2            7             41
  CLUS_3            4             13
  CLUS_4            2             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        4      7      7
  CPS1 WILD-TYPE     37     45     21
D14V2, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             37
  CLUS_2            7             45
  CLUS_3            7             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
  CPS1 MUTATED        5     10      9
  CPS1 WILD-TYPE     53     59     42
D14V3, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            5             53
  CLUS_2           10             59
  CLUS_3            9             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        3      3      1
  CPS1 WILD-TYPE     24     27     16
D14V4, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            3             24
  CLUS_2            3             27
  CLUS_3            1             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
  CPS1 MUTATED        5      7      2      1
  CPS1 WILD-TYPE     27     38     27      5
D14V5, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            5             27
  CLUS_2            7             38
  CLUS_3            2             27
  CLUS_4            1              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CPS1 MUTATED        2      3      5      3      2      0
  CPS1 WILD-TYPE     20     17     19     23     12      6
D14V6, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            3             17
  CLUS_3            5             19
  CLUS_4            3             23
  CLUS_5            2             12
  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
  CPS1 MUTATED        4      9      7      4
  CPS1 WILD-TYPE     36     53     43     22
D14V7, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             36
  CLUS_2            9             53
  CLUS_3            7             43
  CLUS_4            4             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        8     11      5
  CPS1 WILD-TYPE     60     63     31
D14V8, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            8             60
  CLUS_2           11             63
  CLUS_3            5             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CPS1 MUTATED        6      0      5      5      2
  CPS1 WILD-TYPE     87     14     16     19      8
D14V9, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            6             87
  CLUS_2            0             14
  CLUS_3            5             16
  CLUS_4            5             19
  CLUS_5            2              8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CPS1 MUTATED        6      2      6      4
  CPS1 WILD-TYPE     29     49     48     18
D14V10, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            6             29
  CLUS_2            2             49
  CLUS_3            6             48
  CLUS_4            4             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CPS1 MUTATED        2      2      1
  CPS1 WILD-TYPE     14     17     12
D14V11, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            2             17
  CLUS_3            1             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
  CPS1 MUTATED        0      2      3
  CPS1 WILD-TYPE      4     17     22
D14V12, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            2             17
  CLUS_3            3             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        1      5      1      3
  ARID1A WILD-TYPE     36     43     16     16
D15V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               36
  CLUS_2              5               43
  CLUS_3              1               16
  CLUS_4              3               16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        2      5      3
  ARID1A WILD-TYPE     39     47     25
D15V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              2               39
  CLUS_2              5               47
  CLUS_3              3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        6      5      2
  ARID1A WILD-TYPE     52     64     49
D15V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               52
  CLUS_2              5               64
  CLUS_3              2               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        3      2      0
  ARID1A WILD-TYPE     24     28     17
D15V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               24
  CLUS_2              2               28
  CLUS_3              0               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
  ARID1A MUTATED        4      1      1      1
  ARID1A WILD-TYPE     28     44     28      5
D15V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               28
  CLUS_2              1               44
  CLUS_3              1               28
  CLUS_4              1                5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARID1A MUTATED        1      3      1      2      0      0
  ARID1A WILD-TYPE     21     17     23     24     14      6
D15V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               21
  CLUS_2              3               17
  CLUS_3              1               23
  CLUS_4              2               24
  CLUS_5              0               14
  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        0      6      6      1
  ARID1A WILD-TYPE     40     56     44     25
D15V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               40
  CLUS_2              6               56
  CLUS_3              6               44
  CLUS_4              1               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        4      6      3
  ARID1A WILD-TYPE     64     68     33
D15V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               64
  CLUS_2              6               68
  CLUS_3              3               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ARID1A MUTATED        4      1      2      3      1
  ARID1A WILD-TYPE     89     13     19     21      9
D15V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               89
  CLUS_2              1               13
  CLUS_3              2               19
  CLUS_4              3               21
  CLUS_5              1                9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger 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        4      2      3      2
  ARID1A WILD-TYPE     31     49     51     20
D15V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               31
  CLUS_2              2               49
  CLUS_3              3               51
  CLUS_4              2               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      2      0
  ARID1A WILD-TYPE     16     17     13
D15V11, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               46 
      TCGA-21-5782       TCGA-21-5784       TCGA-21-5786       TCGA-22-5471 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5472       TCGA-22-5473       TCGA-22-5474       TCGA-22-5477 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5478       TCGA-22-5480       TCGA-22-5482       TCGA-22-5485 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5489       TCGA-22-5491       TCGA-22-5492       TCGA-33-6737 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5231       TCGA-34-5232       TCGA-34-5234       TCGA-34-5236 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5239       TCGA-34-5927       TCGA-34-5928       TCGA-34-5929 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-37-3783       TCGA-37-5819       TCGA-39-5019       TCGA-39-5024 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-39-5027       TCGA-43-5668       TCGA-43-6143       TCGA-43-6647 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-43-6770       TCGA-43-6771       TCGA-46-6025       TCGA-46-6026 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-56-5897       TCGA-56-5898       TCGA-56-6545       TCGA-56-6546 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2709       TCGA-70-6722       TCGA-70-6723       TCGA-85-6175 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-85-6560       TCGA-85-6561 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        0      0      2
  ARID1A WILD-TYPE      4     19     23
D15V12, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               46 
      TCGA-21-5782       TCGA-21-5784       TCGA-21-5786       TCGA-22-5471 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5472       TCGA-22-5473       TCGA-22-5474       TCGA-22-5477 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5478       TCGA-22-5480       TCGA-22-5482       TCGA-22-5485 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-22-5489       TCGA-22-5491       TCGA-22-5492       TCGA-33-6737 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5231       TCGA-34-5232       TCGA-34-5234       TCGA-34-5236 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-34-5239       TCGA-34-5927       TCGA-34-5928       TCGA-34-5929 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-37-3783       TCGA-37-5819       TCGA-39-5019       TCGA-39-5024 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-39-5027       TCGA-43-5668       TCGA-43-6143       TCGA-43-6647 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-43-6770       TCGA-43-6771       TCGA-46-6025       TCGA-46-6026 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-56-5897       TCGA-56-5898       TCGA-56-6545       TCGA-56-6546 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-60-2709       TCGA-70-6722       TCGA-70-6723       TCGA-85-6175 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-85-6560       TCGA-85-6561 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 

Clustering(16) Variable = SLC28A1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC28A1 MUTATED        0      1      3      0
  SLC28A1 WILD-TYPE     37     47     14     19
D16V1, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                37
  CLUS_2               1                47
  CLUS_3               3                14
  CLUS_4               0                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        0      1      3
  SLC28A1 WILD-TYPE     41     51     25
D16V2, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                41
  CLUS_2               1                51
  CLUS_3               3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        6      1      2
  SLC28A1 WILD-TYPE     52     68     49
D16V3, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               6                52
  CLUS_2               1                68
  CLUS_3               2                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        3      0      2
  SLC28A1 WILD-TYPE     24     30     15
D16V4, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                30
  CLUS_3               2                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
  SLC28A1 MUTATED        2      4      0      0
  SLC28A1 WILD-TYPE     30     41     29      6
D16V5, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               2                30
  CLUS_2               4                41
  CLUS_3               0                29
  CLUS_4               0                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SLC28A1 MUTATED        1      1      2      0      2      0
  SLC28A1 WILD-TYPE     21     19     22     26     12      6
D16V6, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                19
  CLUS_3               2                22
  CLUS_4               0                26
  CLUS_5               2                12
  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
  SLC28A1 MUTATED        3      0      5      1
  SLC28A1 WILD-TYPE     37     62     45     25
D16V7, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               3                37
  CLUS_2               0                62
  CLUS_3               5                45
  CLUS_4               1                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        3      1      5
  SLC28A1 WILD-TYPE     65     73     31
D16V8, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               3                65
  CLUS_2               1                73
  CLUS_3               5                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SLC28A1 MUTATED        4      1      3      0      0
  SLC28A1 WILD-TYPE     89     13     18     24     10
D16V9, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               4                89
  CLUS_2               1                13
  CLUS_3               3                18
  CLUS_4               0                24
  CLUS_5               0                10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC28A1 MUTATED        0      1      3      4
  SLC28A1 WILD-TYPE     35     50     51     18
D16V10, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                35
  CLUS_2               1                50
  CLUS_3               3                51
  CLUS_4               4                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC28A1 MUTATED        2      1      1
  SLC28A1 WILD-TYPE     14     18     12
D16V11, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                18
  CLUS_3               1                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
  SLC28A1 MUTATED        0      0      4
  SLC28A1 WILD-TYPE      4     19     21
D16V12, multiclass
        clus
vv       SLC28A1 MUTATED SLC28A1 WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                19
  CLUS_3               4                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"

Clustering(17) Variable = POLR2B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POLR2B MUTATED        1      2      0      0
  POLR2B WILD-TYPE     36     46     17     19
D17V1, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              1               36
  CLUS_2              2               46
  CLUS_3              0               17
  CLUS_4              0               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLR2B MUTATED        1      2      0
  POLR2B WILD-TYPE     40     50     28
D17V2, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              1               40
  CLUS_2              2               50
  CLUS_3              0               28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLR2B MUTATED        2      2      2
  POLR2B WILD-TYPE     56     67     49
D17V3, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              2               56
  CLUS_2              2               67
  CLUS_3              2               49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLR2B MUTATED        0      1      2
  POLR2B WILD-TYPE     27     29     15
D17V4, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              0               27
  CLUS_2              1               29
  CLUS_3              2               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
  POLR2B MUTATED        1      2      1      0
  POLR2B WILD-TYPE     31     43     28      6
D17V5, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              1               31
  CLUS_2              2               43
  CLUS_3              1               28
  CLUS_4              0                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  POLR2B MUTATED        0      0      2      1      0      1
  POLR2B WILD-TYPE     22     20     22     25     14      5
D17V6, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              0               22
  CLUS_2              0               20
  CLUS_3              2               22
  CLUS_4              1               25
  CLUS_5              0               14
  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
  POLR2B MUTATED        0      2      2      2
  POLR2B WILD-TYPE     40     60     48     24
D17V7, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              0               40
  CLUS_2              2               60
  CLUS_3              2               48
  CLUS_4              2               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLR2B MUTATED        4      2      0
  POLR2B WILD-TYPE     64     72     36
D17V8, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              4               64
  CLUS_2              2               72
  CLUS_3              0               36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  POLR2B MUTATED        2      1      0      0      2
  POLR2B WILD-TYPE     91     13     21     24      8
D17V9, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              2               91
  CLUS_2              1               13
  CLUS_3              0               21
  CLUS_4              0               24
  CLUS_5              2                8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  POLR2B MUTATED        0      1      3      1
  POLR2B WILD-TYPE     35     50     51     21
D17V10, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              0               35
  CLUS_2              1               50
  CLUS_3              3               51
  CLUS_4              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  POLR2B MUTATED        1      1      1
  POLR2B WILD-TYPE     15     18     12
D17V11, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              1               15
  CLUS_2              1               18
  CLUS_3              1               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
  POLR2B MUTATED        1      1      1
  POLR2B WILD-TYPE      3     18     24
D17V12, multiclass
        clus
vv       POLR2B MUTATED POLR2B WILD-TYPE
  CLUS_1              1                3
  CLUS_2              1               18
  CLUS_3              1               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = HRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        2      2      0      0
  HRAS WILD-TYPE     35     46     17     19
D18V1, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            2             35
  CLUS_2            2             46
  CLUS_3            0             17
  CLUS_4            0             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        2      2      0
  HRAS WILD-TYPE     39     50     28
D18V2, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            2             39
  CLUS_2            2             50
  CLUS_3            0             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        0      3      2
  HRAS WILD-TYPE     58     66     49
D18V3, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            0             58
  CLUS_2            3             66
  CLUS_3            2             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        0      2      0
  HRAS WILD-TYPE     27     28     17
D18V4, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             2             72 
    TCGA-18-3417     TCGA-18-4721     TCGA-18-5592     TCGA-18-5595 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5787     TCGA-22-4593 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-4599     TCGA-22-4601     TCGA-22-4613     TCGA-22-5471 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5485 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5489     TCGA-22-5491     TCGA-22-5492     TCGA-33-4566 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-33-4582     TCGA-33-4583     TCGA-33-4586     TCGA-33-6737 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5231     TCGA-34-5232     TCGA-34-5234     TCGA-34-5236 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5239     TCGA-34-5241     TCGA-34-5927     TCGA-34-5928 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5929     TCGA-37-5819     TCGA-39-5016     TCGA-39-5019 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5021     TCGA-39-5022     TCGA-39-5024     TCGA-39-5027 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5028     TCGA-39-5029     TCGA-39-5030     TCGA-39-5031 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5035     TCGA-39-5036     TCGA-39-5037     TCGA-39-5039 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-5668     TCGA-43-6143     TCGA-43-6647     TCGA-43-6770 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-6771     TCGA-46-6025     TCGA-46-6026     TCGA-56-5897 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-56-5898     TCGA-56-6545     TCGA-56-6546     TCGA-60-2709 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-63-5128     TCGA-63-5131     TCGA-63-6202     TCGA-70-6722 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-70-6723     TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        0      1      1      0
  HRAS WILD-TYPE     32     44     28      6
D18V5, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             2            110 
    TCGA-18-4721     TCGA-18-5592     TCGA-18-5595     TCGA-21-1070 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-21-1071     TCGA-21-1076     TCGA-21-1078     TCGA-21-1081 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5787     TCGA-22-1011 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-4591     TCGA-22-4607     TCGA-22-5471     TCGA-22-5472 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5473     TCGA-22-5474     TCGA-22-5477     TCGA-22-5478 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5480     TCGA-22-5482     TCGA-22-5485     TCGA-22-5489 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5491     TCGA-22-5492     TCGA-33-4532     TCGA-33-4547 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-33-4566     TCGA-33-4582     TCGA-33-4586     TCGA-33-6737 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-2596     TCGA-34-2608     TCGA-34-5231     TCGA-34-5232 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5234     TCGA-34-5236     TCGA-34-5239     TCGA-34-5241 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5927     TCGA-34-5928     TCGA-34-5929     TCGA-37-3789 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-37-4133     TCGA-37-4135     TCGA-37-4141     TCGA-37-5819 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5016     TCGA-39-5019     TCGA-39-5021     TCGA-39-5022 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5024     TCGA-39-5027     TCGA-39-5028     TCGA-39-5029 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5030     TCGA-39-5031     TCGA-39-5035     TCGA-39-5037 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-2578     TCGA-43-3394     TCGA-43-5668     TCGA-43-6143 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2698     TCGA-60-2708     TCGA-60-2709     TCGA-60-2710 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2711     TCGA-60-2712     TCGA-60-2713     TCGA-60-2719 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2720     TCGA-60-2721     TCGA-60-2724     TCGA-60-2725 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2726     TCGA-63-5128     TCGA-63-5131     TCGA-63-6202 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2727     TCGA-66-2766     TCGA-66-2767     TCGA-66-2768 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2770     TCGA-66-2773     TCGA-66-2777     TCGA-66-2778 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2781     TCGA-66-2782     TCGA-66-2783     TCGA-66-2785 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2788     TCGA-66-2791     TCGA-66-2794     TCGA-66-2795 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2800     TCGA-70-6722     TCGA-70-6723     TCGA-85-6175 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-85-6560     TCGA-85-6561 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  HRAS MUTATED        0      0      1      1      0      0
  HRAS WILD-TYPE     22     20     23     25     14      6
D18V6, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             2            110 
    TCGA-18-4721     TCGA-18-5592     TCGA-18-5595     TCGA-21-1070 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-21-1071     TCGA-21-1076     TCGA-21-1078     TCGA-21-1081 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5787     TCGA-22-1011 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-4591     TCGA-22-4607     TCGA-22-5471     TCGA-22-5472 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5473     TCGA-22-5474     TCGA-22-5477     TCGA-22-5478 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5480     TCGA-22-5482     TCGA-22-5485     TCGA-22-5489 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5491     TCGA-22-5492     TCGA-33-4532     TCGA-33-4547 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-33-4566     TCGA-33-4582     TCGA-33-4586     TCGA-33-6737 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-2596     TCGA-34-2608     TCGA-34-5231     TCGA-34-5232 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5234     TCGA-34-5236     TCGA-34-5239     TCGA-34-5241 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5927     TCGA-34-5928     TCGA-34-5929     TCGA-37-3789 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-37-4133     TCGA-37-4135     TCGA-37-4141     TCGA-37-5819 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5016     TCGA-39-5019     TCGA-39-5021     TCGA-39-5022 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5024     TCGA-39-5027     TCGA-39-5028     TCGA-39-5029 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5030     TCGA-39-5031     TCGA-39-5035     TCGA-39-5037 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-2578     TCGA-43-3394     TCGA-43-5668     TCGA-43-6143 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2698     TCGA-60-2708     TCGA-60-2709     TCGA-60-2710 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2711     TCGA-60-2712     TCGA-60-2713     TCGA-60-2719 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2720     TCGA-60-2721     TCGA-60-2724     TCGA-60-2725 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2726     TCGA-63-5128     TCGA-63-5131     TCGA-63-6202 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2727     TCGA-66-2766     TCGA-66-2767     TCGA-66-2768 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2770     TCGA-66-2773     TCGA-66-2777     TCGA-66-2778 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2781     TCGA-66-2782     TCGA-66-2783     TCGA-66-2785 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2788     TCGA-66-2791     TCGA-66-2794     TCGA-66-2795 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-66-2800     TCGA-70-6722     TCGA-70-6723     TCGA-85-6175 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-85-6560     TCGA-85-6561 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        1      2      2      0
  HRAS WILD-TYPE     39     60     48     26
D18V7, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            1             39
  CLUS_2            2             60
  CLUS_3            2             48
  CLUS_4            0             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        2      2      1
  HRAS WILD-TYPE     66     72     35
D18V8, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            2             66
  CLUS_2            2             72
  CLUS_3            1             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  HRAS MUTATED        3      0      0      1      1
  HRAS WILD-TYPE     90     14     21     23      9
D18V9, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            3             90
  CLUS_2            0             14
  CLUS_3            0             21
  CLUS_4            1             23
  CLUS_5            1              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  HRAS MUTATED        2      1      2      0
  HRAS WILD-TYPE     33     50     52     22
D18V10, multiclass
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  CLUS_1            2             33
  CLUS_2            1             50
  CLUS_3            2             52
  CLUS_4            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        1      0      0
  HRAS WILD-TYPE     15     19     13
D18V11, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             1             47 
    TCGA-21-5782     TCGA-21-5784     TCGA-22-5471     TCGA-22-5472 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5473     TCGA-22-5474     TCGA-22-5477     TCGA-22-5478 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5480     TCGA-22-5482     TCGA-22-5485     TCGA-22-5489 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5491     TCGA-22-5492     TCGA-33-6737     TCGA-34-5231 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5232     TCGA-34-5234     TCGA-34-5236     TCGA-34-5239 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5927     TCGA-34-5928     TCGA-34-5929     TCGA-37-3783 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-37-5819     TCGA-39-5019     TCGA-39-5022     TCGA-39-5024 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5027     TCGA-43-5668     TCGA-43-6143     TCGA-43-6647 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2709     TCGA-63-6202     TCGA-70-6722     TCGA-70-6723 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  HRAS MUTATED        1      0      0
  HRAS WILD-TYPE      3     19     25
D18V12, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             1             47 
    TCGA-21-5782     TCGA-21-5784     TCGA-22-5471     TCGA-22-5472 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5473     TCGA-22-5474     TCGA-22-5477     TCGA-22-5478 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5480     TCGA-22-5482     TCGA-22-5485     TCGA-22-5489 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-22-5491     TCGA-22-5492     TCGA-33-6737     TCGA-34-5231 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5232     TCGA-34-5234     TCGA-34-5236     TCGA-34-5239 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-34-5927     TCGA-34-5928     TCGA-34-5929     TCGA-37-3783 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-37-5819     TCGA-39-5019     TCGA-39-5022     TCGA-39-5024 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-39-5027     TCGA-43-5668     TCGA-43-6143     TCGA-43-6647 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-43-6770     TCGA-43-6771     TCGA-46-6025     TCGA-46-6026 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-56-5897     TCGA-56-5898     TCGA-56-6545     TCGA-56-6546 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-60-2709     TCGA-63-6202     TCGA-70-6722     TCGA-70-6723 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-85-6175     TCGA-85-6560     TCGA-85-6561 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 

Clustering(19) Variable = PI16 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PI16 MUTATED        0      2      2      1
  PI16 WILD-TYPE     37     46     15     18
D19V1, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            0             37
  CLUS_2            2             46
  CLUS_3            2             15
  CLUS_4            1             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PI16 MUTATED        1      2      2
  PI16 WILD-TYPE     40     50     26
D19V2, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            1             40
  CLUS_2            2             50
  CLUS_3            2             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PI16 MUTATED        1      4      2
  PI16 WILD-TYPE     57     65     49
D19V3, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            1             57
  CLUS_2            4             65
  CLUS_3            2             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PI16 MUTATED        0      4      0
  PI16 WILD-TYPE     27     26     17
D19V4, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            0             27
  CLUS_2            4             26
  CLUS_3            0             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
  PI16 MUTATED        3      0      1      1
  PI16 WILD-TYPE     29     45     28      5
D19V5, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            3             29
  CLUS_2            0             45
  CLUS_3            1             28
  CLUS_4            1              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PI16 MUTATED        1      2      0      1      0      1
  PI16 WILD-TYPE     21     18     24     25     14      5
D19V6, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            2             18
  CLUS_3            0             24
  CLUS_4            1             25
  CLUS_5            0             14
  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
  PI16 MUTATED        1      4      1      1
  PI16 WILD-TYPE     39     58     49     25
D19V7, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            1             39
  CLUS_2            4             58
  CLUS_3            1             49
  CLUS_4            1             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PI16 MUTATED        2      4      1
  PI16 WILD-TYPE     66     70     35
D19V8, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            2             66
  CLUS_2            4             70
  CLUS_3            1             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PI16 MUTATED        2      1      1      2      0
  PI16 WILD-TYPE     91     13     20     22     10
D19V9, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            2             91
  CLUS_2            1             13
  CLUS_3            1             20
  CLUS_4            2             22
  CLUS_5            0             10
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PI16 MUTATED        1      1      4      0
  PI16 WILD-TYPE     34     50     50     22
D19V10, multiclass
        clus
vv       PI16 MUTATED PI16 WILD-TYPE
  CLUS_1            1             34
  CLUS_2            1             50
  CLUS_3            4             50
  CLUS_4            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PI16 MUTATED        0      0      2
  PI16 WILD-TYPE     16     19     11
D19V11, multiclass
[1] "Remove cluster labels:" "PI16 MUTATED"          
clus
  PI16 MUTATED PI16 WILD-TYPE 
             2             46 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-22-5471 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5489 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5492     TCGA-33-6737     TCGA-34-5231     TCGA-34-5232 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-34-5234     TCGA-34-5236     TCGA-34-5239     TCGA-34-5927 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-34-5928     TCGA-34-5929     TCGA-37-3783     TCGA-37-5819 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-39-5019     TCGA-39-5022     TCGA-39-5024     TCGA-39-5027 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-5668     TCGA-43-6143     TCGA-43-6647     TCGA-43-6770 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-6771     TCGA-46-6025     TCGA-46-6026     TCGA-56-5897 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-56-5898     TCGA-56-6545     TCGA-56-6546     TCGA-60-2709 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-63-6202     TCGA-70-6722     TCGA-70-6723     TCGA-85-6175 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-85-6560     TCGA-85-6561 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PI16 MUTATED        0      2      0
  PI16 WILD-TYPE      4     17     25
D19V12, multiclass
[1] "Remove cluster labels:" "PI16 MUTATED"          
clus
  PI16 MUTATED PI16 WILD-TYPE 
             2             46 
    TCGA-21-5782     TCGA-21-5784     TCGA-21-5786     TCGA-22-5471 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5472     TCGA-22-5473     TCGA-22-5474     TCGA-22-5477 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5478     TCGA-22-5480     TCGA-22-5482     TCGA-22-5489 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-22-5492     TCGA-33-6737     TCGA-34-5231     TCGA-34-5232 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-34-5234     TCGA-34-5236     TCGA-34-5239     TCGA-34-5927 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-34-5928     TCGA-34-5929     TCGA-37-3783     TCGA-37-5819 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-39-5019     TCGA-39-5022     TCGA-39-5024     TCGA-39-5027 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-5668     TCGA-43-6143     TCGA-43-6647     TCGA-43-6770 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-43-6771     TCGA-46-6025     TCGA-46-6026     TCGA-56-5897 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-56-5898     TCGA-56-6545     TCGA-56-6546     TCGA-60-2709 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-63-6202     TCGA-70-6722     TCGA-70-6723     TCGA-85-6175 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" "PI16 WILD-TYPE" 
    TCGA-85-6560     TCGA-85-6561 
"PI16 WILD-TYPE" "PI16 WILD-TYPE" 
