[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTCOAD-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/COAD-TP/11590519/COAD-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/10687005/transformed.cor.cli.txt"

nPatients in clinical file=459, in cluster file=154, common to both=154
[1]  27 154
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          107            47 
  APC MUTATED APC WILD-TYPE 
          107            47 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            73             81 
  TP53 MUTATED TP53 WILD-TYPE 
            73             81 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            59             95 
  KRAS MUTATED KRAS WILD-TYPE 
            59             95 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            139 
  NRAS MUTATED NRAS WILD-TYPE 
            15            139 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             136 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             136 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             125 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             125 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             144 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             144 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            20            134 
  BRAF MUTATED BRAF WILD-TYPE 
            20            134 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               135 
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               135 
[1] "MGC42105 MUTATION ANALYSIS"
[1] 3
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                10                144 
  MGC42105 MUTATED MGC42105 WILD-TYPE 
                10                144 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              141 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              13              141 
[1] "DNMT1 MUTATION ANALYSIS"
[1] 3
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             12             142 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             12             142 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             150 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             150 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             10             144 
  CDC27 MUTATED CDC27 WILD-TYPE 
             10             144 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              128 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              128 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
             6            148 
  BCOR MUTATED BCOR WILD-TYPE 
             6            148 
[1] "ZHX2 MUTATION ANALYSIS"
[1] 3
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             8            146 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             8            146 
[1] "KLHL5 MUTATION ANALYSIS"
[1] 3
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              5             149 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              5             149 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             10             144 
  CASP8 MUTATED CASP8 WILD-TYPE 
             10             144 
[1] "PCDHGB1 MUTATION ANALYSIS"
[1] 3
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                7               147 
  PCDHGB1 MUTATED PCDHGB1 WILD-TYPE 
                7               147 
[1] "UBXN11 MUTATION ANALYSIS"
[1] 3
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               3              151 
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               3              151 
[1] "MIER3 MUTATION ANALYSIS"
[1] 3
  MIER3 MUTATED MIER3 WILD-TYPE 
             10             144 
  MIER3 MUTATED MIER3 WILD-TYPE 
             10             144 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                151 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 3                151 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              11              143 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              11              143 
[1] "PCDHGA9 MUTATION ANALYSIS"
[1] 3
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                5               149 
  PCDHGA9 MUTATED PCDHGA9 WILD-TYPE 
                5               149 
[1] "PCDHGA7 MUTATION ANALYSIS"
[1] 3
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                5               149 
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                5               149 
[1] "KLK2 MUTATION ANALYSIS"
[1] 3
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            151 
  KLK2 MUTATED KLK2 WILD-TYPE 
             3            151 
[1] "terrence_modification_tag"
[1] TRUE
[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 154 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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[7] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 154 columns, 0 survival variables, and 9 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_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=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APC MUTATED       18     42     21     17
  APC WILD-TYPE     16     15      7      5
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          18            16
  CLUS_2          42            15
  CLUS_3          21             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
  APC MUTATED       22     50     26
  APC WILD-TYPE     20     19      4
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          22            20
  CLUS_2          50            19
  CLUS_3          26             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       39     52     14
  APC WILD-TYPE     28     13      6
D1V3, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          39            28
  CLUS_2          52            13
  CLUS_3          14             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  APC MUTATED       20     29     12     10
  APC WILD-TYPE      3     18      6      6
D1V4, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          20             3
  CLUS_2          29            18
  CLUS_3          12             6
  CLUS_4          10             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
  APC MUTATED        9     20      3     26      8      5
  APC WILD-TYPE      0     12      3     10      5      3
D1V5, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           9             0
  CLUS_2          20            12
  CLUS_3           3             3
  CLUS_4          26            10
  CLUS_5           8             5
  CLUS_6           5             3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  APC MUTATED       13      6     86
  APC WILD-TYPE      4      5     38
D1V6, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          13             4
  CLUS_2           6             5
  CLUS_3          86            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  APC MUTATED        2      1      0     84     18
  APC WILD-TYPE      2      0      1     27     17
D1V7, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           2             2
  CLUS_2           1             0
  CLUS_3           0             1
  CLUS_4          84            27
  CLUS_5          18            17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
               cls
clus             0  1
  APC MUTATED    3 95
  APC WILD-TYPE  1 42
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      3   95
  APC WILD-TYPE    1   42
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_2           3             1
  CLUS_3          95            42
[1] 2 2
[1] FALSE
               vv
clus            CLUS_1 CLUS_3 CLUS_4
  APC MUTATED        3     24     71
  APC WILD-TYPE      1     12     30
D1V9, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           3             1
  CLUS_3          24            12
  CLUS_4          71            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"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       12     38      9     10
  TP53 WILD-TYPE     22     19     19     12
D2V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             22
  CLUS_2           38             19
  CLUS_3            9             19
  CLUS_4           10             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       12     37     20
  TP53 WILD-TYPE     30     32     10
D2V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             30
  CLUS_2           37             32
  CLUS_3           20             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
  TP53 MUTATED       14     47     11
  TP53 WILD-TYPE     53     18      9
D2V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           14             53
  CLUS_2           47             18
  CLUS_3           11              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        7     24      8      4
  TP53 WILD-TYPE     16     23     10     12
D2V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             16
  CLUS_2           24             23
  CLUS_3            8             10
  CLUS_4            4             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        3     14      3     17      3      3
  TP53 WILD-TYPE      6     18      3     19     10      5
D2V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              6
  CLUS_2           14             18
  CLUS_3            3              3
  CLUS_4           17             19
  CLUS_5            3             10
  CLUS_6            3              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
  TP53 MUTATED       10      2     60
  TP53 WILD-TYPE      7      9     64
D2V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10              7
  CLUS_2            2              9
  CLUS_3           60             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        3      0      0     61      8
  TP53 WILD-TYPE      1      1      1     50     27
D2V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              1
  CLUS_2            0              1
  CLUS_3            0              1
  CLUS_4           61             50
  CLUS_5            8             27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                cls
clus              0  1
  TP53 MUTATED    1 67
  TP53 WILD-TYPE  3 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   67
  TP53 WILD-TYPE    3   70
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_2            1              3
  CLUS_3           67             70
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  TP53 MUTATED        3     16     49
  TP53 WILD-TYPE      1     20     52
D2V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              1
  CLUS_3           16             20
  CLUS_4           49             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = KRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED       10     17     17      7
  KRAS WILD-TYPE     24     40     11     15
D3V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             24
  CLUS_2           17             40
  CLUS_3           17             11
  CLUS_4            7             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
  KRAS MUTATED       16     31      4
  KRAS WILD-TYPE     26     38     26
D3V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16             26
  CLUS_2           31             38
  CLUS_3            4             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
  KRAS MUTATED       28     23      7
  KRAS WILD-TYPE     39     42     13
D3V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           28             39
  CLUS_2           23             42
  CLUS_3            7             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRAS MUTATED        9     22      6      8
  KRAS WILD-TYPE     14     25     12      8
D3V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9             14
  CLUS_2           22             25
  CLUS_3            6             12
  CLUS_4            8              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRAS MUTATED        4     13      3     16      5      4
  KRAS WILD-TYPE      5     19      3     20      8      4
D3V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4              5
  CLUS_2           13             19
  CLUS_3            3              3
  CLUS_4           16             20
  CLUS_5            5              8
  CLUS_6            4              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
  KRAS MUTATED        3      3     51
  KRAS WILD-TYPE     14      8     73
D3V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             14
  CLUS_2            3              8
  CLUS_3           51             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRAS MUTATED        2      1      0     41     13
  KRAS WILD-TYPE      2      0      1     70     22
D3V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2              2
  CLUS_2            1              0
  CLUS_3            0              1
  CLUS_4           41             70
  CLUS_5           13             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                cls
clus              0  1
  KRAS MUTATED    2 51
  KRAS WILD-TYPE  2 86
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2   51
  KRAS WILD-TYPE    2   86
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_2            2              2
  CLUS_3           51             86
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  KRAS MUTATED        1     11     41
  KRAS WILD-TYPE      3     25     60
D3V9, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              3
  CLUS_3           11             25
  CLUS_4           41             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = NRAS MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        0      8      4      2
  NRAS WILD-TYPE     34     49     24     20
D4V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             34
  CLUS_2            8             49
  CLUS_3            4             24
  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
  NRAS MUTATED        2     11      1
  NRAS WILD-TYPE     40     58     29
D4V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             40
  CLUS_2           11             58
  CLUS_3            1             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
  NRAS MUTATED        7      7      1
  NRAS WILD-TYPE     60     58     19
D4V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            7             60
  CLUS_2            7             58
  CLUS_3            1             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NRAS MUTATED        1      8      1      2
  NRAS WILD-TYPE     22     39     17     14
D4V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             22
  CLUS_2            8             39
  CLUS_3            1             17
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NRAS MUTATED        1      4      0      5      2      0
  NRAS WILD-TYPE      8     28      6     31     11      8
D4V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              8
  CLUS_2            4             28
  CLUS_3            0              6
  CLUS_4            5             31
  CLUS_5            2             11
  CLUS_6            0              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NRAS MUTATED        2      0     12
  NRAS WILD-TYPE     15     11    112
D4V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             15
  CLUS_2            0             11
  CLUS_3           12            112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NRAS MUTATED        0      0      0     12      2
  NRAS WILD-TYPE      4      1      1     99     33
D4V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              1
  CLUS_3            0              1
  CLUS_4           12             99
  CLUS_5            2             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                cls
clus               0   1
  NRAS MUTATED     0  13
  NRAS WILD-TYPE   4 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   13
  NRAS WILD-TYPE    4  124
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_2            0              4
  CLUS_3           13            124
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  NRAS MUTATED        0      3     10
  NRAS WILD-TYPE      4     33     91
D4V9, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              4
  CLUS_3            3             33
  CLUS_4           10             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = SMAD4 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD4 MUTATED        6      4      5      2
  SMAD4 WILD-TYPE     28     53     23     20
D5V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             6              28
  CLUS_2             4              53
  CLUS_3             5              23
  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
  SMAD4 MUTATED        7      9      1
  SMAD4 WILD-TYPE     35     60     29
D5V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             7              35
  CLUS_2             9              60
  CLUS_3             1              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
  SMAD4 MUTATED       12      2      4
  SMAD4 WILD-TYPE     55     63     16
D5V3, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1            12              55
  CLUS_2             2              63
  CLUS_3             4              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
  SMAD4 MUTATED        3      8      2      1
  SMAD4 WILD-TYPE     20     39     16     15
D5V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             8              39
  CLUS_3             2              16
  CLUS_4             1              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 CLUS_4 CLUS_5 CLUS_6
  SMAD4 MUTATED        2      5      1      3      1      2
  SMAD4 WILD-TYPE      7     27      5     33     12      6
D5V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2               7
  CLUS_2             5              27
  CLUS_3             1               5
  CLUS_4             3              33
  CLUS_5             1              12
  CLUS_6             2               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
  SMAD4 MUTATED        1      0     16
  SMAD4 WILD-TYPE     16     11    108
D5V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             0              11
  CLUS_3            16             108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD4 MUTATED        0      0      0     11      6
  SMAD4 WILD-TYPE      4      1      1    100     29
D5V7, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4            11             100
  CLUS_5             6              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  17
  SMAD4 WILD-TYPE   4 120
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   17
  SMAD4 WILD-TYPE    4  120
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_2             0               4
  CLUS_3            17             120
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  SMAD4 MUTATED        0      5     12
  SMAD4 WILD-TYPE      4     31     89
D5V9, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               4
  CLUS_3             5              31
  CLUS_4            12              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBXW7 MUTATED       10      7      5      3
  FBXW7 WILD-TYPE     24     50     23     19
D6V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            10              24
  CLUS_2             7              50
  CLUS_3             5              23
  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
  FBXW7 MUTATED       12     11      2
  FBXW7 WILD-TYPE     30     58     28
D6V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            12              30
  CLUS_2            11              58
  CLUS_3             2              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
  FBXW7 MUTATED       21      5      3
  FBXW7 WILD-TYPE     46     60     17
D6V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            21              46
  CLUS_2             5              60
  CLUS_3             3              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
  FBXW7 MUTATED        4      8      1      9
  FBXW7 WILD-TYPE     19     39     17      7
D6V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              19
  CLUS_2             8              39
  CLUS_3             1              17
  CLUS_4             9               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FBXW7 MUTATED        1      6      2      5      6      2
  FBXW7 WILD-TYPE      8     26      4     31      7      6
D6V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             6              26
  CLUS_3             2               4
  CLUS_4             5              31
  CLUS_5             6               7
  CLUS_6             2               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
  FBXW7 MUTATED        2      2     25
  FBXW7 WILD-TYPE     15      9     99
D6V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2              15
  CLUS_2             2               9
  CLUS_3            25              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FBXW7 MUTATED        1      0      0     14     14
  FBXW7 WILD-TYPE      3      1      1     97     21
D6V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4            14              97
  CLUS_5            14              21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  27
  FBXW7 WILD-TYPE   4 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   27
  FBXW7 WILD-TYPE    4  110
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_2             0               4
  CLUS_3            27             110
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  FBXW7 MUTATED        2      5     20
  FBXW7 WILD-TYPE      2     31     81
D6V9, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             2               2
  CLUS_3             5              31
  CLUS_4            20              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = SMAD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD2 MUTATED        3      1      4      1
  SMAD2 WILD-TYPE     31     56     24     21
D7V1, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             3              31
  CLUS_2             1              56
  CLUS_3             4              24
  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
  SMAD2 MUTATED        5      4      0
  SMAD2 WILD-TYPE     37     65     30
D7V2, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             5              37
  CLUS_2             4              65
  CLUS_3             0              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
  SMAD2 MUTATED        8      1      1
  SMAD2 WILD-TYPE     59     64     19
D7V3, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             8              59
  CLUS_2             1              64
  CLUS_3             1              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SMAD2 MUTATED        2      3      1      1
  SMAD2 WILD-TYPE     21     44     17     15
D7V4, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             3              44
  CLUS_3             1              17
  CLUS_4             1              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 CLUS_4 CLUS_5 CLUS_6
  SMAD2 MUTATED        0      2      0      3      1      1
  SMAD2 WILD-TYPE      9     30      6     33     12      7
D7V5, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              30
  CLUS_3             0               6
  CLUS_4             3              33
  CLUS_5             1              12
  CLUS_6             1               7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SMAD2 MUTATED        0      0     10
  SMAD2 WILD-TYPE     17     11    114
D7V6, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             0              11
  CLUS_3            10             114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SMAD2 MUTATED        0      0      0      7      3
  SMAD2 WILD-TYPE      4      1      1    104     32
D7V7, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4             7             104
  CLUS_5             3              32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED     0   9
  SMAD2 WILD-TYPE   4 128
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      0    9
  SMAD2 WILD-TYPE    4  128
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             9             128
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  SMAD2 MUTATED        0      2      7
  SMAD2 WILD-TYPE      4     34     94
D7V9, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               4
  CLUS_3             2              34
  CLUS_4             7              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED       14      1      3      0
  BRAF WILD-TYPE     20     56     25     22
D8V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           14             20
  CLUS_2            1             56
  CLUS_3            3             25
  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
  BRAF MUTATED       15      2      1
  BRAF WILD-TYPE     27     67     29
D8V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           15             27
  CLUS_2            2             67
  CLUS_3            1             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
  BRAF MUTATED       17      1      2
  BRAF WILD-TYPE     50     64     18
D8V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           17             50
  CLUS_2            1             64
  CLUS_3            2             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        3      4      3      1
  BRAF WILD-TYPE     20     43     15     15
D8V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             20
  CLUS_2            4             43
  CLUS_3            3             15
  CLUS_4            1             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 CLUS_4 CLUS_5 CLUS_6
  BRAF MUTATED        1      3      2      3      1      1
  BRAF WILD-TYPE      8     29      4     33     12      7
D8V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1              8
  CLUS_2            3             29
  CLUS_3            2              4
  CLUS_4            3             33
  CLUS_5            1             12
  CLUS_6            1              7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        0      6     14
  BRAF WILD-TYPE     17      5    110
D8V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0             17
  CLUS_2            6              5
  CLUS_3           14            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BRAF MUTATED        0      0      1      4     15
  BRAF WILD-TYPE      4      1      0    107     20
D8V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              1
  CLUS_3            1              0
  CLUS_4            4            107
  CLUS_5           15             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                cls
clus               0   1
  BRAF MUTATED     1  19
  BRAF WILD-TYPE   3 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1   19
  BRAF WILD-TYPE    3  118
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_2            1              3
  CLUS_3           19            118
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  BRAF MUTATED        0      1     19
  BRAF WILD-TYPE      4     35     82
D8V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              4
  CLUS_3            1             35
  CLUS_4           19             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = FAM123B MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM123B MUTATED        8      6      4      1
  FAM123B WILD-TYPE     26     51     24     21
D9V1, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               8                26
  CLUS_2               6                51
  CLUS_3               4                24
  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
  FAM123B MUTATED        9      8      2
  FAM123B WILD-TYPE     33     61     28
D9V2, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               9                33
  CLUS_2               8                61
  CLUS_3               2                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
  FAM123B MUTATED       14      4      0
  FAM123B WILD-TYPE     53     61     20
D9V3, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1              14                53
  CLUS_2               4                61
  CLUS_3               0                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM123B MUTATED        2      4      1      4
  FAM123B WILD-TYPE     21     43     17     12
D9V4, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                21
  CLUS_2               4                43
  CLUS_3               1                17
  CLUS_4               4                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FAM123B MUTATED        1      4      0      2      4      0
  FAM123B WILD-TYPE      8     28      6     34      9      8
D9V5, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               4                28
  CLUS_3               0                 6
  CLUS_4               2                34
  CLUS_5               4                 9
  CLUS_6               0                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM123B MUTATED        0      2     17
  FAM123B WILD-TYPE     17      9    107
D9V6, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                 9
  CLUS_3              17               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FAM123B MUTATED        0      0      0     11      8
  FAM123B WILD-TYPE      4      1      1    100     27
D9V7, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 1
  CLUS_3               0                 1
  CLUS_4              11               100
  CLUS_5               8                27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  FAM123B MUTATED     1  17
  FAM123B WILD-TYPE   3 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      1   17
  FAM123B WILD-TYPE    3  120
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_2               1                 3
  CLUS_3              17               120
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_3 CLUS_4
  FAM123B MUTATED        1      3     14
  FAM123B WILD-TYPE      3     33     87
D9V9, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                 3
  CLUS_3               3                33
  CLUS_4              14                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MGC42105 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MGC42105 MUTATED        7      1      2      0
  MGC42105 WILD-TYPE     27     56     26     22
D10V1, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                7                 27
  CLUS_2                1                 56
  CLUS_3                2                 26
  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
  MGC42105 MUTATED        6      3      1
  MGC42105 WILD-TYPE     36     66     29
D10V2, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                6                 36
  CLUS_2                3                 66
  CLUS_3                1                 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
  MGC42105 MUTATED        7      2      1
  MGC42105 WILD-TYPE     60     63     19
D10V3, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                2                 63
  CLUS_3                1                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MGC42105 MUTATED        0      3      1      2
  MGC42105 WILD-TYPE     23     44     17     14
D10V4, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                0                 23
  CLUS_2                3                 44
  CLUS_3                1                 17
  CLUS_4                2                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MGC42105 MUTATED        1      0      0      2      2      1
  MGC42105 WILD-TYPE      8     32      6     34     11      7
D10V5, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                0                 32
  CLUS_3                0                  6
  CLUS_4                2                 34
  CLUS_5                2                 11
  CLUS_6                1                  7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  MGC42105 MUTATED        0      2      7
  MGC42105 WILD-TYPE     17      9    117
D10V6, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                2                  9
  CLUS_3                7                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MGC42105 MUTATED        0      0      0      4      5
  MGC42105 WILD-TYPE      4      1      1    107     30
D10V7, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  1
  CLUS_3                0                  1
  CLUS_4                4                107
  CLUS_5                5                 30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                    cls
clus                   0   1
  MGC42105 MUTATED     0  10
  MGC42105 WILD-TYPE   4 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MGC42105 MUTATED      0   10
  MGC42105 WILD-TYPE    4  127
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_2                0                  4
  CLUS_3               10                127
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_3 CLUS_4
  MGC42105 MUTATED        0      1      9
  MGC42105 WILD-TYPE      4     35     92
D10V9, multiclass
        clus
vv       MGC42105 MUTATED MGC42105 WILD-TYPE
  CLUS_1                0                  4
  CLUS_3                1                 35
  CLUS_4                9                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = ACVR1B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ACVR1B MUTATED        4      2      3      1
  ACVR1B WILD-TYPE     30     55     25     21
D11V1, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              4               30
  CLUS_2              2               55
  CLUS_3              3               25
  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
  ACVR1B MUTATED        5      5      0
  ACVR1B WILD-TYPE     37     64     30
D11V2, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              5               37
  CLUS_2              5               64
  CLUS_3              0               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
  ACVR1B MUTATED       11      1      1
  ACVR1B WILD-TYPE     56     64     19
D11V3, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1             11               56
  CLUS_2              1               64
  CLUS_3              1               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ACVR1B MUTATED        2      5      1      3
  ACVR1B WILD-TYPE     21     42     17     13
D11V4, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              2               21
  CLUS_2              5               42
  CLUS_3              1               17
  CLUS_4              3               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ACVR1B MUTATED        1      1      1      5      2      1
  ACVR1B WILD-TYPE      8     31      5     31     11      7
D11V5, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              1                8
  CLUS_2              1               31
  CLUS_3              1                5
  CLUS_4              5               31
  CLUS_5              2               11
  CLUS_6              1                7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ACVR1B MUTATED        0      3     10
  ACVR1B WILD-TYPE     17      8    114
D11V6, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              0               17
  CLUS_2              3                8
  CLUS_3             10              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ACVR1B MUTATED        0      0      0      6      7
  ACVR1B WILD-TYPE      4      1      1    105     28
D11V7, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                1
  CLUS_3              0                1
  CLUS_4              6              105
  CLUS_5              7               28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED     0  13
  ACVR1B WILD-TYPE   4 124
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED      0   13
  ACVR1B WILD-TYPE    4  124
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_2              0                4
  CLUS_3             13              124
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_3 CLUS_4
  ACVR1B MUTATED        1      2     10
  ACVR1B WILD-TYPE      3     34     91
D11V9, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              1                3
  CLUS_3              2               34
  CLUS_4             10               91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = DNMT1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT1 MUTATED        6      1      3      1
  DNMT1 WILD-TYPE     28     56     25     21
D12V1, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             6              28
  CLUS_2             1              56
  CLUS_3             3              25
  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
  DNMT1 MUTATED        8      2      1
  DNMT1 WILD-TYPE     34     67     29
D12V2, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             8              34
  CLUS_2             2              67
  CLUS_3             1              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
  DNMT1 MUTATED        9      2      1
  DNMT1 WILD-TYPE     58     63     19
D12V3, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             9              58
  CLUS_2             2              63
  CLUS_3             1              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DNMT1 MUTATED        1      3      0      4
  DNMT1 WILD-TYPE     22     44     18     12
D12V4, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             1              22
  CLUS_2             3              44
  CLUS_3             0              18
  CLUS_4             4              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  DNMT1 MUTATED        1      2      0      2      3      0
  DNMT1 WILD-TYPE      8     30      6     34     10      8
D12V5, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              30
  CLUS_3             0               6
  CLUS_4             2              34
  CLUS_5             3              10
  CLUS_6             0               8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DNMT1 MUTATED        1      2      9
  DNMT1 WILD-TYPE     16      9    115
D12V6, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             2               9
  CLUS_3             9             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  DNMT1 MUTATED        1      0      0      4      7
  DNMT1 WILD-TYPE      3      1      1    107     28
D12V7, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4             4             107
  CLUS_5             7              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                 cls
clus                0   1
  DNMT1 MUTATED     0  10
  DNMT1 WILD-TYPE   4 127
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED      0   10
  DNMT1 WILD-TYPE    4  127
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_2             0               4
  CLUS_3            10             127
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  DNMT1 MUTATED        2      0      8
  DNMT1 WILD-TYPE      2     36     93
D12V9, multiclass
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  CLUS_1             2               2
  CLUS_3             0              36
  CLUS_4             8              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = PCBP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCBP1 MUTATED        0      2      2      0
  PCBP1 WILD-TYPE     34     55     26     22
D13V1, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              34
  CLUS_2             2              55
  CLUS_3             2              26
  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
  PCBP1 MUTATED        0      3      1
  PCBP1 WILD-TYPE     42     66     29
D13V2, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             3              66
  CLUS_3             1              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
  PCBP1 MUTATED        1      3      0
  PCBP1 WILD-TYPE     66     62     20
D13V3, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             1              66
  CLUS_2             3              62
  CLUS_3             0              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCBP1 MUTATED        0      2      0      0
  PCBP1 WILD-TYPE     23     45     18     16
D13V4, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2             102 
     TCGA-A6-2672      TCGA-A6-2676      TCGA-A6-2677      TCGA-A6-2678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3519      TCGA-AA-3520 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3525      TCGA-AA-3529 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3664      TCGA-AA-3672      TCGA-AA-3678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3688      TCGA-AA-3695      TCGA-AA-3696 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3831      TCGA-AA-3833 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3848 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3971 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3982 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00Q      TCGA-AA-A00R 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A022 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCBP1 MUTATED        0      0      0      2      0      0
  PCBP1 WILD-TYPE      9     32      6     34     13      8
D13V5, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2             102 
     TCGA-A6-2672      TCGA-A6-2676      TCGA-A6-2677      TCGA-A6-2678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3519      TCGA-AA-3520 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3525      TCGA-AA-3529 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3664      TCGA-AA-3672      TCGA-AA-3678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3688      TCGA-AA-3695      TCGA-AA-3696 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3831      TCGA-AA-3833 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3848 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3971 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3982 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00Q      TCGA-AA-A00R 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A022 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PCBP1 MUTATED        0      0      4
  PCBP1 WILD-TYPE     17     11    120
D13V6, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             0              11
  CLUS_3             4             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCBP1 MUTATED        0      0      0      4      0
  PCBP1 WILD-TYPE      4      1      1    107     35
D13V7, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4             4             107
  CLUS_5             0              35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     0   3
  PCBP1 WILD-TYPE   4 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      0    3
  PCBP1 WILD-TYPE    4  134
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             3             134
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  PCBP1 MUTATED        0      0      3
  PCBP1 WILD-TYPE      4     36     98
D13V9, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0               4
  CLUS_3             0              36
  CLUS_4             3              98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = CDC27 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDC27 MUTATED        5      0      4      0
  CDC27 WILD-TYPE     29     57     24     22
D14V1, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             5              29
  CLUS_2             0              57
  CLUS_3             4              24
  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
  CDC27 MUTATED        6      2      1
  CDC27 WILD-TYPE     36     67     29
D14V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             6              36
  CLUS_2             2              67
  CLUS_3             1              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
  CDC27 MUTATED        9      0      1
  CDC27 WILD-TYPE     58     65     19
D14V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             9              58
  CLUS_2             0              65
  CLUS_3             1              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDC27 MUTATED        2      4      1      1
  CDC27 WILD-TYPE     21     43     17     15
D14V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             4              43
  CLUS_3             1              17
  CLUS_4             1              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 CLUS_4 CLUS_5 CLUS_6
  CDC27 MUTATED        1      2      0      4      1      0
  CDC27 WILD-TYPE      8     30      6     32     12      8
D14V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              30
  CLUS_3             0               6
  CLUS_4             4              32
  CLUS_5             1              12
  CLUS_6             0               8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CDC27 MUTATED        1      1      8
  CDC27 WILD-TYPE     16     10    116
D14V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             1              10
  CLUS_3             8             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDC27 MUTATED        0      0      1      4      5
  CDC27 WILD-TYPE      4      1      0    107     30
D14V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               1
  CLUS_3             1               0
  CLUS_4             4             107
  CLUS_5             5              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                 cls
clus                0   1
  CDC27 MUTATED     1   6
  CDC27 WILD-TYPE   3 131
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    6
  CDC27 WILD-TYPE    3  131
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_2             1               3
  CLUS_3             6             131
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  CDC27 MUTATED        2      1      4
  CDC27 WILD-TYPE      2     35     97
D14V9, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               2
  CLUS_3             1              35
  CLUS_4             4              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        6      5      6      4
  PIK3CA WILD-TYPE     28     52     22     18
D15V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               28
  CLUS_2              5               52
  CLUS_3              6               22
  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
  PIK3CA MUTATED        8     10      3
  PIK3CA WILD-TYPE     34     59     27
D15V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               34
  CLUS_2             10               59
  CLUS_3              3               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
  PIK3CA MUTATED       18      5      2
  PIK3CA WILD-TYPE     49     60     18
D15V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             18               49
  CLUS_2              5               60
  CLUS_3              2               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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      8      1      4
  PIK3CA WILD-TYPE     15     39     17     12
D15V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               15
  CLUS_2              8               39
  CLUS_3              1               17
  CLUS_4              4               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PIK3CA MUTATED        3      5      1      7      3      2
  PIK3CA WILD-TYPE      6     27      5     29     10      6
D15V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3                6
  CLUS_2              5               27
  CLUS_3              1                5
  CLUS_4              7               29
  CLUS_5              3               10
  CLUS_6              2                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
  PIK3CA MUTATED        1      3     22
  PIK3CA WILD-TYPE     16      8    102
D15V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               16
  CLUS_2              3                8
  CLUS_3             22              102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PIK3CA MUTATED        1      0      0     17      8
  PIK3CA WILD-TYPE      3      1      1     94     27
D15V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                3
  CLUS_2              0                1
  CLUS_3              0                1
  CLUS_4             17               94
  CLUS_5              8               27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  22
  PIK3CA WILD-TYPE   3 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   22
  PIK3CA WILD-TYPE    3  115
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_2              1                3
  CLUS_3             22              115
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_3 CLUS_4
  PIK3CA MUTATED        1      3     19
  PIK3CA WILD-TYPE      3     33     82
D15V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                3
  CLUS_3              3               33
  CLUS_4             19               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = BCOR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BCOR MUTATED        3      0      2      0
  BCOR WILD-TYPE     31     57     26     22
D16V1, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            3             31
  CLUS_2            0             57
  CLUS_3            2             26
  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
  BCOR MUTATED        4      1      0
  BCOR WILD-TYPE     38     68     30
D16V2, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            4             38
  CLUS_2            1             68
  CLUS_3            0             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
  BCOR MUTATED        6      0      0
  BCOR WILD-TYPE     61     65     20
D16V3, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            6             61
  CLUS_2            0             65
  CLUS_3            0             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BCOR MUTATED        0      4      0      2
  BCOR WILD-TYPE     23     43     18     14
D16V4, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            0             23
  CLUS_2            4             43
  CLUS_3            0             18
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  BCOR MUTATED        0      1      1      3      1      0
  BCOR WILD-TYPE      9     31      5     33     12      8
D16V5, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1             31
  CLUS_3            1              5
  CLUS_4            3             33
  CLUS_5            1             12
  CLUS_6            0              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCOR MUTATED        0      0      6
  BCOR WILD-TYPE     17     11    118
D16V6, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            0             17
  CLUS_2            0             11
  CLUS_3            6            118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  BCOR MUTATED        0      0      0      2      4
  BCOR WILD-TYPE      4      1      1    109     31
D16V7, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              1
  CLUS_3            0              1
  CLUS_4            2            109
  CLUS_5            4             31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                cls
clus               0   1
  BCOR MUTATED     0   5
  BCOR WILD-TYPE   4 132
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED      0    5
  BCOR WILD-TYPE    4  132
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_2            0              4
  CLUS_3            5            132
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  BCOR MUTATED        1      0      4
  BCOR WILD-TYPE      3     36     97
D16V9, multiclass
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  CLUS_1            1              3
  CLUS_3            0             36
  CLUS_4            4             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = ZHX2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZHX2 MUTATED        4      2      1      0
  ZHX2 WILD-TYPE     30     55     27     22
D17V1, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            4             30
  CLUS_2            2             55
  CLUS_3            1             27
  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
  ZHX2 MUTATED        4      3      0
  ZHX2 WILD-TYPE     38     66     30
D17V2, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            4             38
  CLUS_2            3             66
  CLUS_3            0             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
  ZHX2 MUTATED        6      2      0
  ZHX2 WILD-TYPE     61     63     20
D17V3, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            6             61
  CLUS_2            2             63
  CLUS_3            0             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZHX2 MUTATED        0      3      0      2
  ZHX2 WILD-TYPE     23     44     18     14
D17V4, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            0             23
  CLUS_2            3             44
  CLUS_3            0             18
  CLUS_4            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ZHX2 MUTATED        0      1      0      2      2      0
  ZHX2 WILD-TYPE      9     31      6     34     11      8
D17V5, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1             31
  CLUS_3            0              6
  CLUS_4            2             34
  CLUS_5            2             11
  CLUS_6            0              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ZHX2 MUTATED        0      0      8
  ZHX2 WILD-TYPE     17     11    116
D17V6, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            0             17
  CLUS_2            0             11
  CLUS_3            8            116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ZHX2 MUTATED        0      0      0      3      5
  ZHX2 WILD-TYPE      4      1      1    108     30
D17V7, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              1
  CLUS_3            0              1
  CLUS_4            3            108
  CLUS_5            5             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                cls
clus               0   1
  ZHX2 MUTATED     0   6
  ZHX2 WILD-TYPE   4 131
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED      0    6
  ZHX2 WILD-TYPE    4  131
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_2            0              4
  CLUS_3            6            131
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  ZHX2 MUTATED        1      1      4
  ZHX2 WILD-TYPE      3     35     97
D17V9, multiclass
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  CLUS_1            1              3
  CLUS_3            1             35
  CLUS_4            4             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = KLHL5 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLHL5 MUTATED        2      1      2      0
  KLHL5 WILD-TYPE     32     56     26     22
D18V1, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             2              32
  CLUS_2             1              56
  CLUS_3             2              26
  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
  KLHL5 MUTATED        2      1      2
  KLHL5 WILD-TYPE     40     68     28
D18V2, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             1              68
  CLUS_3             2              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
  KLHL5 MUTATED        4      1      0
  KLHL5 WILD-TYPE     63     64     20
D18V3, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             4              63
  CLUS_2             1              64
  CLUS_3             0              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLHL5 MUTATED        0      2      0      2
  KLHL5 WILD-TYPE     23     45     18     14
D18V4, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             0              23
  CLUS_2             2              45
  CLUS_3             0              18
  CLUS_4             2              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KLHL5 MUTATED        0      2      0      1      1      0
  KLHL5 WILD-TYPE      9     30      6     35     12      8
D18V5, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              30
  CLUS_3             0               6
  CLUS_4             1              35
  CLUS_5             1              12
  CLUS_6             0               8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KLHL5 MUTATED        0      0      5
  KLHL5 WILD-TYPE     17     11    119
D18V6, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             0              11
  CLUS_3             5             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KLHL5 MUTATED        0      0      0      4      1
  KLHL5 WILD-TYPE      4      1      1    107     34
D18V7, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4             4             107
  CLUS_5             1              34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                 cls
clus                0   1
  KLHL5 MUTATED     0   4
  KLHL5 WILD-TYPE   4 133
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      0    4
  KLHL5 WILD-TYPE    4  133
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             4             133
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  KLHL5 MUTATED        1      1      2
  KLHL5 WILD-TYPE      3     35     99
D18V9, multiclass
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  CLUS_1             1               3
  CLUS_3             1              35
  CLUS_4             2              99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = CASP8 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CASP8 MUTATED        7      0      2      0
  CASP8 WILD-TYPE     27     57     26     22
D19V1, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             7              27
  CLUS_2             0              57
  CLUS_3             2              26
  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
  CASP8 MUTATED        9      0      0
  CASP8 WILD-TYPE     33     69     30
D19V2, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             9              33
  CLUS_2             0              69
  CLUS_3             0              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
  CASP8 MUTATED       10      0      0
  CASP8 WILD-TYPE     57     65     20
D19V3, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1            10              57
  CLUS_2             0              65
  CLUS_3             0              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CASP8 MUTATED        4      1      0      3
  CASP8 WILD-TYPE     19     46     18     13
D19V4, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             4              19
  CLUS_2             1              46
  CLUS_3             0              18
  CLUS_4             3              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CASP8 MUTATED        1      2      1      1      3      0
  CASP8 WILD-TYPE      8     30      5     35     10      8
D19V5, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             2              30
  CLUS_3             1               5
  CLUS_4             1              35
  CLUS_5             3              10
  CLUS_6             0               8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CASP8 MUTATED        0      1      9
  CASP8 WILD-TYPE     17     10    115
D19V6, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             0              17
  CLUS_2             1              10
  CLUS_3             9             115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CASP8 MUTATED        0      0      0      0     10
  CASP8 WILD-TYPE      4      1      1    111     25
D19V7, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4             0             111
  CLUS_5            10              25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                 cls
clus                0   1
  CASP8 MUTATED     0   8
  CASP8 WILD-TYPE   4 129
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      0    8
  CASP8 WILD-TYPE    4  129
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             8             129
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  CASP8 MUTATED        1      0      7
  CASP8 WILD-TYPE      3     36     94
D19V9, multiclass
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  CLUS_1             1               3
  CLUS_3             0              36
  CLUS_4             7              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = PCDHGB1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHGB1 MUTATED        3      1      3      0
  PCDHGB1 WILD-TYPE     31     56     25     22
D20V1, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               3                31
  CLUS_2               1                56
  CLUS_3               3                25
  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
  PCDHGB1 MUTATED        4      2      1
  PCDHGB1 WILD-TYPE     38     67     29
D20V2, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               4                38
  CLUS_2               2                67
  CLUS_3               1                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
  PCDHGB1 MUTATED        6      1      0
  PCDHGB1 WILD-TYPE     61     64     20
D20V3, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               6                61
  CLUS_2               1                64
  CLUS_3               0                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHGB1 MUTATED        1      2      0      2
  PCDHGB1 WILD-TYPE     22     45     18     14
D20V4, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               1                22
  CLUS_2               2                45
  CLUS_3               0                18
  CLUS_4               2                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCDHGB1 MUTATED        0      2      0      2      1      0
  PCDHGB1 WILD-TYPE      9     30      6     34     12      8
D20V5, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                30
  CLUS_3               0                 6
  CLUS_4               2                34
  CLUS_5               1                12
  CLUS_6               0                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHGB1 MUTATED        0      1      6
  PCDHGB1 WILD-TYPE     17     10    118
D20V6, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               1                10
  CLUS_3               6               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCDHGB1 MUTATED        0      0      0      4      3
  PCDHGB1 WILD-TYPE      4      1      1    107     32
D20V7, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 1
  CLUS_3               0                 1
  CLUS_4               4               107
  CLUS_5               3                32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                   cls
clus                  0   1
  PCDHGB1 MUTATED     0   6
  PCDHGB1 WILD-TYPE   4 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGB1 MUTATED      0    6
  PCDHGB1 WILD-TYPE    4  131
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_2               0                 4
  CLUS_3               6               131
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_3 CLUS_4
  PCDHGB1 MUTATED        1      1      4
  PCDHGB1 WILD-TYPE      3     35     97
D20V9, multiclass
        clus
vv       PCDHGB1 MUTATED PCDHGB1 WILD-TYPE
  CLUS_1               1                 3
  CLUS_3               1                35
  CLUS_4               4                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = UBXN11 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UBXN11 MUTATED        2      0      0      0
  UBXN11 WILD-TYPE     32     57     28     22
D21V1, multiclass
[1] "Remove cluster labels:" "UBXN11 MUTATED"        
clus
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               2              139 
      TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2677 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-A6-3810       TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3696 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3930 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3949       TCGA-AA-3952 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3971 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01Q       TCGA-AA-A024 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AY-4070       TCGA-AY-4071 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  UBXN11 MUTATED        2      0      0
  UBXN11 WILD-TYPE     40     69     30
D21V2, multiclass
[1] "Remove cluster labels:" "UBXN11 MUTATED"        
clus
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               2              139 
      TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2677 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-A6-3810       TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3696 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3930 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3949       TCGA-AA-3952 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3971 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01Q       TCGA-AA-A024 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AY-4070       TCGA-AY-4071 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  UBXN11 MUTATED        3      0      0
  UBXN11 WILD-TYPE     64     65     20
D21V3, multiclass
        clus
vv       UBXN11 MUTATED UBXN11 WILD-TYPE
  CLUS_1              3               64
  CLUS_2              0               65
  CLUS_3              0               20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  UBXN11 MUTATED        1      1      0      0
  UBXN11 WILD-TYPE     22     46     18     16
D21V4, multiclass
[1] "Remove cluster labels:" "UBXN11 MUTATED"        
clus
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               2              102 
      TCGA-A6-2672       TCGA-A6-2676       TCGA-A6-2677       TCGA-A6-2678 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3810 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3519       TCGA-AA-3520 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3521       TCGA-AA-3522       TCGA-AA-3525       TCGA-AA-3529 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532       TCGA-AA-3534 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3664       TCGA-AA-3672       TCGA-AA-3678 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3688       TCGA-AA-3695       TCGA-AA-3696 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3831 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3844       TCGA-AA-3845 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3852       TCGA-AA-3854 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3930       TCGA-AA-3955       TCGA-AA-3971 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3982 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-A004       TCGA-AA-A00A 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00Q       TCGA-AA-A00R 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01I 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01S 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A022 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  UBXN11 MUTATED        0      0      1      1      0      0
  UBXN11 WILD-TYPE      9     32      5     35     13      8
D21V5, multiclass
[1] "Remove cluster labels:" "UBXN11 MUTATED"        
clus
  UBXN11 MUTATED UBXN11 WILD-TYPE 
               2              102 
      TCGA-A6-2672       TCGA-A6-2676       TCGA-A6-2677       TCGA-A6-2678 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808       TCGA-A6-3810 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3519       TCGA-AA-3520 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3521       TCGA-AA-3522       TCGA-AA-3525       TCGA-AA-3529 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532       TCGA-AA-3534 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3664       TCGA-AA-3672       TCGA-AA-3678 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3688       TCGA-AA-3695       TCGA-AA-3696 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3831 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3844       TCGA-AA-3845 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3852       TCGA-AA-3854 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3869 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3930       TCGA-AA-3955       TCGA-AA-3971 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3982 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-A004       TCGA-AA-A00A 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00Q       TCGA-AA-A00R 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01I 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01S 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A022 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J 
"UBXN11 WILD-TYPE" "UBXN11 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  UBXN11 MUTATED        0      1      2
  UBXN11 WILD-TYPE     17     10    122
D21V6, multiclass
        clus
vv       UBXN11 MUTATED UBXN11 WILD-TYPE
  CLUS_1              0               17
  CLUS_2              1               10
  CLUS_3              2              122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  UBXN11 MUTATED        0      0      0      0      3
  UBXN11 WILD-TYPE      4      1      1    111     32
D21V7, multiclass
        clus
vv       UBXN11 MUTATED UBXN11 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                1
  CLUS_3              0                1
  CLUS_4              0              111
  CLUS_5              3               32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                  cls
clus                 0   1
  UBXN11 MUTATED     0   3
  UBXN11 WILD-TYPE   4 134
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBXN11 MUTATED      0    3
  UBXN11 WILD-TYPE    4  134
        clus
vv       UBXN11 MUTATED UBXN11 WILD-TYPE
  CLUS_2              0                4
  CLUS_3              3              134
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_3 CLUS_4
  UBXN11 MUTATED        0      0      3
  UBXN11 WILD-TYPE      4     36     98
D21V9, multiclass
        clus
vv       UBXN11 MUTATED UBXN11 WILD-TYPE
  CLUS_1              0                4
  CLUS_3              0               36
  CLUS_4              3               98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = MIER3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MIER3 MUTATED        6      0      3      0
  MIER3 WILD-TYPE     28     57     25     22
D22V1, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             6              28
  CLUS_2             0              57
  CLUS_3             3              25
  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
  MIER3 MUTATED        7      1      1
  MIER3 WILD-TYPE     35     68     29
D22V2, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             7              35
  CLUS_2             1              68
  CLUS_3             1              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
  MIER3 MUTATED        9      0      1
  MIER3 WILD-TYPE     58     65     19
D22V3, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             9              58
  CLUS_2             0              65
  CLUS_3             1              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MIER3 MUTATED        2      4      0      1
  MIER3 WILD-TYPE     21     43     18     15
D22V4, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             4              43
  CLUS_3             0              18
  CLUS_4             1              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 CLUS_4 CLUS_5 CLUS_6
  MIER3 MUTATED        0      4      0      3      0      0
  MIER3 WILD-TYPE      9     28      6     33     13      8
D22V5, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4              28
  CLUS_3             0               6
  CLUS_4             3              33
  CLUS_5             0              13
  CLUS_6             0               8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MIER3 MUTATED        1      1      8
  MIER3 WILD-TYPE     16     10    116
D22V6, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             1              16
  CLUS_2             1              10
  CLUS_3             8             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MIER3 MUTATED        1      0      0      3      6
  MIER3 WILD-TYPE      3      1      1    108     29
D22V7, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             0               1
  CLUS_3             0               1
  CLUS_4             3             108
  CLUS_5             6              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                 cls
clus                0   1
  MIER3 MUTATED     0  10
  MIER3 WILD-TYPE   4 127
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED      0   10
  MIER3 WILD-TYPE    4  127
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_2             0               4
  CLUS_3            10             127
[1] 2 2
[1] FALSE
                 vv
clus              CLUS_1 CLUS_3 CLUS_4
  MIER3 MUTATED        1      1      8
  MIER3 WILD-TYPE      3     35     93
D22V9, multiclass
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  CLUS_1             1               3
  CLUS_3             1              35
  CLUS_4             8              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = TBC1D10C MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TBC1D10C MUTATED        1      0      1      1
  TBC1D10C WILD-TYPE     33     57     27     21
D23V1, multiclass
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_1                1                 33
  CLUS_2                0                 57
  CLUS_3                1                 27
  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
  TBC1D10C MUTATED        2      0      1
  TBC1D10C WILD-TYPE     40     69     29
D23V2, multiclass
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                0                 69
  CLUS_3                1                 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
  TBC1D10C MUTATED        2      1      0
  TBC1D10C WILD-TYPE     65     64     20
D23V3, multiclass
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                1                 64
  CLUS_3                0                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TBC1D10C MUTATED        1      0      0      0
  TBC1D10C WILD-TYPE     22     47     18     16
D23V4, multiclass
[1] "Remove cluster labels:" "TBC1D10C MUTATED"      
clus
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 1                103 
        TCGA-A6-2672         TCGA-A6-2676         TCGA-A6-2677 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2683         TCGA-A6-3807 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-A6-3808         TCGA-A6-3810         TCGA-AA-3514 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3519         TCGA-AA-3520 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3525 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3548 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3558         TCGA-AA-3560 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3678         TCGA-AA-3681 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3695         TCGA-AA-3696 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3715         TCGA-AA-3811 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3818 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3831         TCGA-AA-3833 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3844         TCGA-AA-3845 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3852 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3856         TCGA-AA-3864 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3869         TCGA-AA-3872 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3947         TCGA-AA-3955 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3986         TCGA-AA-3989 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00E 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00Q 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01I 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A022 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A024         TCGA-AA-A029         TCGA-AA-A02F 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02O 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A03J 
"TBC1D10C WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TBC1D10C MUTATED        0      1      0      0      0      0
  TBC1D10C WILD-TYPE      9     31      6     36     13      8
D23V5, multiclass
[1] "Remove cluster labels:" "TBC1D10C MUTATED"      
clus
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 1                103 
        TCGA-A6-2672         TCGA-A6-2676         TCGA-A6-2677 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2683         TCGA-A6-3807 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-A6-3808         TCGA-A6-3810         TCGA-AA-3514 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3519         TCGA-AA-3520 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3525 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3548 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3558         TCGA-AA-3560 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3678         TCGA-AA-3681 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3695         TCGA-AA-3696 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3715         TCGA-AA-3811 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3818 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3831         TCGA-AA-3833 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3844         TCGA-AA-3845 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3852 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3856         TCGA-AA-3864 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3869         TCGA-AA-3872 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3947         TCGA-AA-3955 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3986         TCGA-AA-3989 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00E 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00Q 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01I 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A022 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A024         TCGA-AA-A029         TCGA-AA-A02F 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02O 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" "TBC1D10C WILD-TYPE" 
        TCGA-AA-A03J 
"TBC1D10C WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  TBC1D10C MUTATED        0      1      2
  TBC1D10C WILD-TYPE     17     10    122
D23V6, multiclass
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                1                 10
  CLUS_3                2                122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TBC1D10C MUTATED        0      0      0      1      2
  TBC1D10C WILD-TYPE      4      1      1    110     33
D23V7, multiclass
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                0                  1
  CLUS_3                0                  1
  CLUS_4                1                110
  CLUS_5                2                 33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     0   3
  TBC1D10C WILD-TYPE   4 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      0    3
  TBC1D10C WILD-TYPE    4  134
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_2                0                  4
  CLUS_3                3                134
[1] 2 2
[1] FALSE
                    vv
clus                 CLUS_1 CLUS_3 CLUS_4
  TBC1D10C MUTATED        0      0      3
  TBC1D10C WILD-TYPE      4     36     98
D23V9, multiclass
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  CLUS_1                0                  4
  CLUS_3                0                 36
  CLUS_4                3                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = TCF7L2 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCF7L2 MUTATED        3      1      3      1
  TCF7L2 WILD-TYPE     31     56     25     21
D24V1, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              3               31
  CLUS_2              1               56
  CLUS_3              3               25
  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
  TCF7L2 MUTATED        2      4      2
  TCF7L2 WILD-TYPE     40     65     28
D24V2, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              2               40
  CLUS_2              4               65
  CLUS_3              2               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
  TCF7L2 MUTATED        6      4      1
  TCF7L2 WILD-TYPE     61     61     19
D24V3, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              6               61
  CLUS_2              4               61
  CLUS_3              1               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TCF7L2 MUTATED        1      5      1      1
  TCF7L2 WILD-TYPE     22     42     17     15
D24V4, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               22
  CLUS_2              5               42
  CLUS_3              1               17
  CLUS_4              1               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 CLUS_4 CLUS_5 CLUS_6
  TCF7L2 MUTATED        1      3      0      4      0      0
  TCF7L2 WILD-TYPE      8     29      6     32     13      8
D24V5, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              3               29
  CLUS_3              0                6
  CLUS_4              4               32
  CLUS_5              0               13
  CLUS_6              0                8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  TCF7L2 MUTATED        0      0     10
  TCF7L2 WILD-TYPE     17     11    114
D24V6, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0               17
  CLUS_2              0               11
  CLUS_3             10              114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TCF7L2 MUTATED        0      0      0      8      2
  TCF7L2 WILD-TYPE      4      1      1    103     33
D24V7, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              0                1
  CLUS_3              0                1
  CLUS_4              8              103
  CLUS_5              2               33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED     0   9
  TCF7L2 WILD-TYPE   4 128
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      0    9
  TCF7L2 WILD-TYPE    4  128
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_2              0                4
  CLUS_3              9              128
[1] 2 2
[1] FALSE
                  vv
clus               CLUS_1 CLUS_3 CLUS_4
  TCF7L2 MUTATED        1      2      6
  TCF7L2 WILD-TYPE      3     34     95
D24V9, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1                3
  CLUS_3              2               34
  CLUS_4              6               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = PCDHGA9 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHGA9 MUTATED        2      1      2      0
  PCDHGA9 WILD-TYPE     32     56     26     22
D25V1, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               2                32
  CLUS_2               1                56
  CLUS_3               2                26
  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
  PCDHGA9 MUTATED        3      2      0
  PCDHGA9 WILD-TYPE     39     67     30
D25V2, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               3                39
  CLUS_2               2                67
  CLUS_3               0                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
  PCDHGA9 MUTATED        3      1      1
  PCDHGA9 WILD-TYPE     64     64     19
D25V3, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               3                64
  CLUS_2               1                64
  CLUS_3               1                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHGA9 MUTATED        1      1      0      1
  PCDHGA9 WILD-TYPE     22     46     18     15
D25V4, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               1                22
  CLUS_2               1                46
  CLUS_3               0                18
  CLUS_4               1                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 CLUS_4 CLUS_5 CLUS_6
  PCDHGA9 MUTATED        0      3      0      0      0      0
  PCDHGA9 WILD-TYPE      9     29      6     36     13      8
D25V5, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               3                29
  CLUS_3               0                 6
  CLUS_4               0                36
  CLUS_5               0                13
  CLUS_6               0                 8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHGA9 MUTATED        0      1      4
  PCDHGA9 WILD-TYPE     17     10    120
D25V6, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               1                10
  CLUS_3               4               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCDHGA9 MUTATED        0      0      0      2      3
  PCDHGA9 WILD-TYPE      4      1      1    109     32
D25V7, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 1
  CLUS_3               0                 1
  CLUS_4               2               109
  CLUS_5               3                32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                   cls
clus                  0   1
  PCDHGA9 MUTATED     0   5
  PCDHGA9 WILD-TYPE   4 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA9 MUTATED      0    5
  PCDHGA9 WILD-TYPE    4  132
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_2               0                 4
  CLUS_3               5               132
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_3 CLUS_4
  PCDHGA9 MUTATED        0      1      4
  PCDHGA9 WILD-TYPE      4     35     97
D25V9, multiclass
        clus
vv       PCDHGA9 MUTATED PCDHGA9 WILD-TYPE
  CLUS_1               0                 4
  CLUS_3               1                35
  CLUS_4               4                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = PCDHGA7 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHGA7 MUTATED        2      1      1      1
  PCDHGA7 WILD-TYPE     32     56     27     21
D26V1, multiclass
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_1               2                32
  CLUS_2               1                56
  CLUS_3               1                27
  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
  PCDHGA7 MUTATED        2      2      1
  PCDHGA7 WILD-TYPE     40     67     29
D26V2, multiclass
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_1               2                40
  CLUS_2               2                67
  CLUS_3               1                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
  PCDHGA7 MUTATED        3      1      1
  PCDHGA7 WILD-TYPE     64     64     19
D26V3, multiclass
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_1               3                64
  CLUS_2               1                64
  CLUS_3               1                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCDHGA7 MUTATED        1      0      0      1
  PCDHGA7 WILD-TYPE     22     47     18     15
D26V4, multiclass
[1] "Remove cluster labels:" "PCDHGA7 MUTATED"       
clus
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                2               102 
       TCGA-A6-2672        TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-A6-2683        TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3810 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3519        TCGA-AA-3520 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3525        TCGA-AA-3529 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532        TCGA-AA-3534 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3672        TCGA-AA-3681 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3831        TCGA-AA-3833 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3848 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3856 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3872 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3947        TCGA-AA-3955        TCGA-AA-3971 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3982 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-A004        TCGA-AA-A00A 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A00L        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01I        TCGA-AA-A01K 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A022 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PCDHGA7 MUTATED        0      1      0      0      1      0
  PCDHGA7 WILD-TYPE      9     31      6     36     12      8
D26V5, multiclass
[1] "Remove cluster labels:" "PCDHGA7 MUTATED"       
clus
  PCDHGA7 MUTATED PCDHGA7 WILD-TYPE 
                2               102 
       TCGA-A6-2672        TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-A6-2683        TCGA-A6-3807        TCGA-A6-3808        TCGA-A6-3810 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3519        TCGA-AA-3520 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3525        TCGA-AA-3529 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532        TCGA-AA-3534 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3548        TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3672        TCGA-AA-3681 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3831        TCGA-AA-3833 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3848 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3856 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3872 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3947        TCGA-AA-3955        TCGA-AA-3971 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3982 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-A004        TCGA-AA-A00A 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A00L        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01I        TCGA-AA-A01K 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A022 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J 
"PCDHGA7 WILD-TYPE" "PCDHGA7 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  PCDHGA7 MUTATED        0      1      4
  PCDHGA7 WILD-TYPE     17     10    120
D26V6, multiclass
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_1               0                17
  CLUS_2               1                10
  CLUS_3               4               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PCDHGA7 MUTATED        0      0      0      3      2
  PCDHGA7 WILD-TYPE      4      1      1    108     33
D26V7, multiclass
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               0                 1
  CLUS_3               0                 1
  CLUS_4               3               108
  CLUS_5               2                33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                   cls
clus                  0   1
  PCDHGA7 MUTATED     0   4
  PCDHGA7 WILD-TYPE   4 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA7 MUTATED      0    4
  PCDHGA7 WILD-TYPE    4  133
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_2               0                 4
  CLUS_3               4               133
[1] 2 2
[1] FALSE
                   vv
clus                CLUS_1 CLUS_3 CLUS_4
  PCDHGA7 MUTATED        0      2      2
  PCDHGA7 WILD-TYPE      4     34     99
D26V9, multiclass
        clus
vv       PCDHGA7 MUTATED PCDHGA7 WILD-TYPE
  CLUS_1               0                 4
  CLUS_3               2                34
  CLUS_4               2                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = KLK2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLK2 MUTATED        2      1      0      0
  KLK2 WILD-TYPE     32     56     28     22
D27V1, multiclass
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  CLUS_1            2             32
  CLUS_2            1             56
  CLUS_3            0             28
  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
  KLK2 MUTATED        2      0      1
  KLK2 WILD-TYPE     40     69     29
D27V2, multiclass
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  CLUS_1            2             40
  CLUS_2            0             69
  CLUS_3            1             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
  KLK2 MUTATED        2      1      0
  KLK2 WILD-TYPE     65     64     20
D27V3, multiclass
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  CLUS_1            2             65
  CLUS_2            1             64
  CLUS_3            0             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KLK2 MUTATED        0      1      0      1
  KLK2 WILD-TYPE     23     46     18     15
D27V4, multiclass
[1] "Remove cluster labels:" "KLK2 MUTATED"          
clus
  KLK2 MUTATED KLK2 WILD-TYPE 
             2            102 
    TCGA-A6-2672     TCGA-A6-2676     TCGA-A6-2677     TCGA-A6-2678 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3810 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3519     TCGA-AA-3520 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3521     TCGA-AA-3522     TCGA-AA-3525     TCGA-AA-3529 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532     TCGA-AA-3534 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3672     TCGA-AA-3678     TCGA-AA-3681 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3831     TCGA-AA-3833 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3848 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3856 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3930     TCGA-AA-3947     TCGA-AA-3955     TCGA-AA-3971 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3982 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-A004     TCGA-AA-A00E 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00N     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01I     TCGA-AA-A01K 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A022 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KLK2 MUTATED        0      0      0      1      1      0
  KLK2 WILD-TYPE      9     32      6     35     12      8
D27V5, multiclass
[1] "Remove cluster labels:" "KLK2 MUTATED"          
clus
  KLK2 MUTATED KLK2 WILD-TYPE 
             2            102 
    TCGA-A6-2672     TCGA-A6-2676     TCGA-A6-2677     TCGA-A6-2678 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3810 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3519     TCGA-AA-3520 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3521     TCGA-AA-3522     TCGA-AA-3525     TCGA-AA-3529 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532     TCGA-AA-3534 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3672     TCGA-AA-3678     TCGA-AA-3681 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3831     TCGA-AA-3833 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3848 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3856 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3930     TCGA-AA-3947     TCGA-AA-3955     TCGA-AA-3971 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3982 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-A004     TCGA-AA-A00E 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00N     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01I     TCGA-AA-A01K 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A022 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  KLK2 MUTATED        0      0      3
  KLK2 WILD-TYPE     17     11    121
D27V6, multiclass
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  CLUS_1            0             17
  CLUS_2            0             11
  CLUS_3            3            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KLK2 MUTATED        0      0      0      1      2
  KLK2 WILD-TYPE      4      1      1    110     33
D27V7, multiclass
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0              1
  CLUS_3            0              1
  CLUS_4            1            110
  CLUS_5            2             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                cls
clus               0   1
  KLK2 MUTATED     0   2
  KLK2 WILD-TYPE   4 135
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK2 MUTATED      0    2
  KLK2 WILD-TYPE    4  135
        clus
vv       KLK2 MUTATED KLK2 WILD-TYPE
  CLUS_2            0              4
  CLUS_3            2            135
[1] 2 2
[1] FALSE
                vv
clus             CLUS_1 CLUS_3 CLUS_4
  KLK2 MUTATED        0      1      1
  KLK2 WILD-TYPE      4     35    100
D27V9, multiclass
[1] "Remove cluster labels:" "KLK2 MUTATED"          
clus
  KLK2 MUTATED KLK2 WILD-TYPE 
             2            139 
    TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2677 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-A6-3810     TCGA-AA-3514     TCGA-AA-3516     TCGA-AA-3517 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3543 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3556     TCGA-AA-3558 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562     TCGA-AA-3664 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3672     TCGA-AA-3673 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688     TCGA-AA-3692 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3710 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860     TCGA-AA-3864 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3866     TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3977     TCGA-AA-3979     TCGA-AA-3980 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3982     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A00D     TCGA-AA-A00J     TCGA-AA-A00L 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00U     TCGA-AA-A00W 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02Y     TCGA-AA-A03F 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
    TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"KLK2 WILD-TYPE" "KLK2 WILD-TYPE" "KLK2 WILD-TYPE" 
