[1] "ofn"        "-oTSARC-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/SARC-TP/20140640/SARC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/19898602/transformed.cor.cli.txt"

nPatients in clinical file=260, in cluster file=245, common to both=244
[1] "Reduce the number of clustering variables from 24 to 23."
[1]  23 244
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            84            160 
  TP53 MUTATED TP53 WILD-TYPE 
            84            160 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            37            207 
  ATRX MUTATED ATRX WILD-TYPE 
            37            207 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           24           220 
  RB1 MUTATED RB1 WILD-TYPE 
           24           220 
[1] "NUMBL MUTATION ANALYSIS"
[1] 3
  NUMBL MUTATED NUMBL WILD-TYPE 
              9             235 
  NUMBL MUTATED NUMBL WILD-TYPE 
              9             235 
[1] "MSH3 MUTATION ANALYSIS"
[1] 3
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            237 
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            237 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              6             238 
  EOMES MUTATED EOMES WILD-TYPE 
              6             238 
[1] "PKD2 MUTATION ANALYSIS"
[1] 3
  PKD2 MUTATED PKD2 WILD-TYPE 
             6            238 
  PKD2 MUTATED PKD2 WILD-TYPE 
             6            238 
[1] "LTBP3 MUTATION ANALYSIS"
[1] 3
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             239 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             239 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                8               236 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                8               236 
[1] "WNK1 MUTATION ANALYSIS"
[1] 3
  WNK1 MUTATED WNK1 WILD-TYPE 
             6            238 
  WNK1 MUTATED WNK1 WILD-TYPE 
             6            238 
[1] "ANP32E MUTATION ANALYSIS"
[1] 3
  ANP32E MUTATED ANP32E WILD-TYPE 
               4              240 
  ANP32E MUTATED ANP32E WILD-TYPE 
               4              240 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            237 
  PTEN MUTATED PTEN WILD-TYPE 
             7            237 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                237 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                237 
[1] "TRAF7 MUTATION ANALYSIS"
[1] 3
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             240 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             240 
[1] "MEGF9 MUTATION ANALYSIS"
[1] 3
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             241 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             241 
[1] "LOR MUTATION ANALYSIS"
[1] 3
  LOR MUTATED LOR WILD-TYPE 
            6           238 
  LOR MUTATED LOR WILD-TYPE 
            6           238 
[1] "CABLES1 MUTATION ANALYSIS"
[1] 3
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               241 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               241 
[1] "COL18A1 MUTATION ANALYSIS"
[1] 3
  COL18A1 MUTATED COL18A1 WILD-TYPE 
                7               237 
  COL18A1 MUTATED COL18A1 WILD-TYPE 
                7               237 
[1] "LHCGR MUTATION ANALYSIS"
[1] 3
  LHCGR MUTATED LHCGR WILD-TYPE 
              6             238 
  LHCGR MUTATED LHCGR WILD-TYPE 
              6             238 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           10           234 
  NF1 MUTATED NF1 WILD-TYPE 
           10           234 
[1] "FOXD2 MUTATION ANALYSIS"
[1] 3
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              3             241 
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              3             241 
[1] "MMP17 MUTATION ANALYSIS"
[1] 3
  MMP17 MUTATED MMP17 WILD-TYPE 
              3             241 
  MMP17 MUTATED MMP17 WILD-TYPE 
              3             241 
[1] "ASTE1 MUTATION ANALYSIS"
[1] 3
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              3             241 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              3             241 
[1] "data2feature, selection=ALL"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 244 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
NULL
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
NULL
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 244 columns, 0 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
NULL
[1] "* non-survival variables: "
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=7, 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=7, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=8, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       27     24     30      1
  TP53 WILD-TYPE     35     59     40     24
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           27             35
  CLUS_2           24             59
  CLUS_3           30             40
  CLUS_4            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        9     14     33      6     19      2      1
  TP53 WILD-TYPE     36     32     24     29     26     11      2
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             36
  CLUS_2           14             32
  CLUS_3           33             24
  CLUS_4            6             29
  CLUS_5           19             26
  CLUS_6            2             11
  CLUS_7            1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       11     15     26     20
  TP53 WILD-TYPE     44     27     28     36
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11             44
  CLUS_2           15             27
  CLUS_3           26             28
  CLUS_4           20             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TP53 MUTATED        5     10     18     28      4      7
  TP53 WILD-TYPE     20     24     28     33     15     15
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             20
  CLUS_2           10             24
  CLUS_3           18             28
  CLUS_4           28             33
  CLUS_5            4             15
  CLUS_6            7             15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       36     36     11
  TP53 WILD-TYPE     73     35     51
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           36             73
  CLUS_2           36             35
  CLUS_3           11             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED       12      8     25      4      9     11     14
  TP53 WILD-TYPE     30     15     22     42     17     14     19
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             30
  CLUS_2            8             15
  CLUS_3           25             22
  CLUS_4            4             42
  CLUS_5            9             17
  CLUS_6           11             14
  CLUS_7           14             19
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       26     12     46
  TP53 WILD-TYPE     76     37     46
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           26             76
  CLUS_2           12             37
  CLUS_3           46             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       23      8     49      4
  TP53 WILD-TYPE     53     42     46     18
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           23             53
  CLUS_2            8             42
  CLUS_3           49             46
  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
  TP53 MUTATED       18     30     15
  TP53 WILD-TYPE     61     30     31
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18             61
  CLUS_2           30             30
  CLUS_3           15             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TP53 MUTATED        4      6     17     12      6      9      5      4
  TP53 WILD-TYPE     20     23     16     12      5     12     16     18
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             20
  CLUS_2            6             23
  CLUS_3           17             16
  CLUS_4           12             12
  CLUS_5            6              5
  CLUS_6            9             12
  CLUS_7            5             16
  CLUS_8            4             18
[1] 8 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 = ATRX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED       15      2     17      2
  ATRX WILD-TYPE     47     81     53     23
D2V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           15             47
  CLUS_2            2             81
  CLUS_3           17             53
  CLUS_4            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ATRX MUTATED       13      4      7      2     10      1      0
  ATRX WILD-TYPE     32     42     50     33     35     12      3
D2V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           13             32
  CLUS_2            4             42
  CLUS_3            7             50
  CLUS_4            2             33
  CLUS_5           10             35
  CLUS_6            1             12
  CLUS_7            0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED        9     11      5      6
  ATRX WILD-TYPE     46     31     49     50
D2V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            9             46
  CLUS_2           11             31
  CLUS_3            5             49
  CLUS_4            6             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ATRX MUTATED        5      5      8      8      4      1
  ATRX WILD-TYPE     20     29     38     53     15     21
D2V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            5             20
  CLUS_2            5             29
  CLUS_3            8             38
  CLUS_4            8             53
  CLUS_5            4             15
  CLUS_6            1             21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED       21      9      7
  ATRX WILD-TYPE     88     62     55
D2V5, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           21             88
  CLUS_2            9             62
  CLUS_3            7             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ATRX MUTATED       10      2      3      5      4      6      7
  ATRX WILD-TYPE     32     21     44     41     22     19     26
D2V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           10             32
  CLUS_2            2             21
  CLUS_3            3             44
  CLUS_4            5             41
  CLUS_5            4             22
  CLUS_6            6             19
  CLUS_7            7             26
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED       17      9     11
  ATRX WILD-TYPE     85     40     81
D2V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           17             85
  CLUS_2            9             40
  CLUS_3           11             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED       16      9     12      0
  ATRX WILD-TYPE     60     41     83     22
D2V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           16             60
  CLUS_2            9             41
  CLUS_3           12             83
  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
  ATRX MUTATED       14      8      8
  ATRX WILD-TYPE     65     52     38
D2V9, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           14             65
  CLUS_2            8             52
  CLUS_3            8             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 CLUS_6 CLUS_7 CLUS_8
  ATRX MUTATED        5      7      4      5      1      5      3      0
  ATRX WILD-TYPE     19     22     29     19     10     16     18     22
D2V10, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            5             19
  CLUS_2            7             22
  CLUS_3            4             29
  CLUS_4            5             19
  CLUS_5            1             10
  CLUS_6            5             16
  CLUS_7            3             18
  CLUS_8            0             22
[1] 8 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 = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED       11      7      4      1
  RB1 WILD-TYPE     51     76     66     24
D3V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          11            51
  CLUS_2           7            76
  CLUS_3           4            66
  CLUS_4           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RB1 MUTATED        3      3     13      1      2      1      1
  RB1 WILD-TYPE     42     43     44     34     43     12      2
D3V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            42
  CLUS_2           3            43
  CLUS_3          13            44
  CLUS_4           1            34
  CLUS_5           2            43
  CLUS_6           1            12
  CLUS_7           1             2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        3      1      9      6
  RB1 WILD-TYPE     52     41     45     50
D3V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            52
  CLUS_2           1            41
  CLUS_3           9            45
  CLUS_4           6            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  RB1 MUTATED        2      3      2     10      1      1
  RB1 WILD-TYPE     23     31     44     51     18     21
D3V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            23
  CLUS_2           3            31
  CLUS_3           2            44
  CLUS_4          10            51
  CLUS_5           1            18
  CLUS_6           1            21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        8     15      1
  RB1 WILD-TYPE    101     56     61
D3V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           8           101
  CLUS_2          15            56
  CLUS_3           1            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RB1 MUTATED        3      2     12      2      0      3      2
  RB1 WILD-TYPE     39     21     35     44     26     22     31
D3V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            39
  CLUS_2           2            21
  CLUS_3          12            35
  CLUS_4           2            44
  CLUS_5           0            26
  CLUS_6           3            22
  CLUS_7           2            31
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        0      6     18
  RB1 WILD-TYPE    102     43     74
D3V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0           102
  CLUS_2           6            43
  CLUS_3          18            74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        1      4     19      0
  RB1 WILD-TYPE     75     46     76     22
D3V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            75
  CLUS_2           4            46
  CLUS_3          19            76
  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
  RB1 MUTATED        0     11      7
  RB1 WILD-TYPE     79     49     39
D3V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            79
  CLUS_2          11            49
  CLUS_3           7            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  RB1 MUTATED        3      0      6      7      2      0      0      0
  RB1 WILD-TYPE     21     29     27     17      9     21     21     22
D3V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            21
  CLUS_2           0            29
  CLUS_3           6            27
  CLUS_4           7            17
  CLUS_5           2             9
  CLUS_6           0            21
  CLUS_7           0            21
  CLUS_8           0            22
[1] 8 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 = NUMBL MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUMBL MUTATED        2      2      5      0
  NUMBL WILD-TYPE     60     81     65     25
D4V1, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             2              60
  CLUS_2             2              81
  CLUS_3             5              65
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NUMBL MUTATED        0      2      1      1      4      1      0
  NUMBL WILD-TYPE     45     44     56     34     41     12      3
D4V2, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             0              45
  CLUS_2             2              44
  CLUS_3             1              56
  CLUS_4             1              34
  CLUS_5             4              41
  CLUS_6             1              12
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUMBL MUTATED        2      2      2      2
  NUMBL WILD-TYPE     53     40     52     54
D4V3, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             2              53
  CLUS_2             2              40
  CLUS_3             2              52
  CLUS_4             2              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NUMBL MUTATED        0      0      5      2      1      0
  NUMBL WILD-TYPE     25     34     41     59     18     22
D4V4, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             0              25
  CLUS_2             0              34
  CLUS_3             5              41
  CLUS_4             2              59
  CLUS_5             1              18
  CLUS_6             0              22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUMBL MUTATED        4      2      3
  NUMBL WILD-TYPE    105     69     59
D4V5, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             4             105
  CLUS_2             2              69
  CLUS_3             3              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NUMBL MUTATED        1      0      1      2      3      1      1
  NUMBL WILD-TYPE     41     23     46     44     23     24     32
D4V6, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              23
  CLUS_3             1              46
  CLUS_4             2              44
  CLUS_5             3              23
  CLUS_6             1              24
  CLUS_7             1              32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NUMBL MUTATED        5      1      3
  NUMBL WILD-TYPE     97     48     89
D4V7, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             5              97
  CLUS_2             1              48
  CLUS_3             3              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUMBL MUTATED        4      1      3      1
  NUMBL WILD-TYPE     72     49     92     21
D4V8, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             4              72
  CLUS_2             1              49
  CLUS_3             3              92
  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
  NUMBL MUTATED        5      0      2
  NUMBL WILD-TYPE     74     60     44
D4V9, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             5              74
  CLUS_2             0              60
  CLUS_3             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NUMBL MUTATED        1      0      0      2      0      4      0      0
  NUMBL WILD-TYPE     23     29     33     22     11     17     21     22
D4V10, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             1              23
  CLUS_2             0              29
  CLUS_3             0              33
  CLUS_4             2              22
  CLUS_5             0              11
  CLUS_6             4              17
  CLUS_7             0              21
  CLUS_8             0              22
[1] 8 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 = MSH3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MSH3 MUTATED        0      4      2      1
  MSH3 WILD-TYPE     62     79     68     24
D5V1, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            0             62
  CLUS_2            4             79
  CLUS_3            2             68
  CLUS_4            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MSH3 MUTATED        1      2      1      0      1      1      1
  MSH3 WILD-TYPE     44     44     56     35     44     12      2
D5V2, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            1             44
  CLUS_2            2             44
  CLUS_3            1             56
  CLUS_4            0             35
  CLUS_5            1             44
  CLUS_6            1             12
  CLUS_7            1              2
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MSH3 MUTATED        2      1      1      2
  MSH3 WILD-TYPE     53     41     53     54
D5V3, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             53
  CLUS_2            1             41
  CLUS_3            1             53
  CLUS_4            2             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MSH3 MUTATED        1      2      1      1      0      1
  MSH3 WILD-TYPE     24     32     45     60     19     21
D5V4, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            1             24
  CLUS_2            2             32
  CLUS_3            1             45
  CLUS_4            1             60
  CLUS_5            0             19
  CLUS_6            1             21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MSH3 MUTATED        4      2      1
  MSH3 WILD-TYPE    105     69     61
D5V5, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            4            105
  CLUS_2            2             69
  CLUS_3            1             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MSH3 MUTATED        0      3      1      1      1      1      0
  MSH3 WILD-TYPE     42     20     46     45     25     24     33
D5V6, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            3             20
  CLUS_3            1             46
  CLUS_4            1             45
  CLUS_5            1             25
  CLUS_6            1             24
  CLUS_7            0             33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MSH3 MUTATED        2      2      2
  MSH3 WILD-TYPE    100     47     90
D5V7, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2            100
  CLUS_2            2             47
  CLUS_3            2             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MSH3 MUTATED        2      2      2      0
  MSH3 WILD-TYPE     74     48     93     22
D5V8, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             74
  CLUS_2            2             48
  CLUS_3            2             93
  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
  MSH3 MUTATED        2      0      2
  MSH3 WILD-TYPE     77     60     44
D5V9, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             77
  CLUS_2            0             60
  CLUS_3            2             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MSH3 MUTATED        1      1      0      0      0      0      2      0
  MSH3 WILD-TYPE     23     28     33     24     11     21     19     22
D5V10, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            1             23
  CLUS_2            1             28
  CLUS_3            0             33
  CLUS_4            0             24
  CLUS_5            0             11
  CLUS_6            0             21
  CLUS_7            2             19
  CLUS_8            0             22
[1] 8 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 = EOMES MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EOMES MUTATED        1      3      2      0
  EOMES WILD-TYPE     61     80     68     25
D6V1, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              61
  CLUS_2             3              80
  CLUS_3             2              68
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  EOMES MUTATED        1      1      1      1      1      1      0
  EOMES WILD-TYPE     44     45     56     34     44     12      3
D6V2, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              44
  CLUS_2             1              45
  CLUS_3             1              56
  CLUS_4             1              34
  CLUS_5             1              44
  CLUS_6             1              12
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EOMES MUTATED        1      1      0      2
  EOMES WILD-TYPE     54     41     54     54
D6V3, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              54
  CLUS_2             1              41
  CLUS_3             0              54
  CLUS_4             2              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  EOMES MUTATED        1      0      2      1      0      0
  EOMES WILD-TYPE     24     34     44     60     19     22
D6V4, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              24
  CLUS_2             0              34
  CLUS_3             2              44
  CLUS_4             1              60
  CLUS_5             0              19
  CLUS_6             0              22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        3      2      1
  EOMES WILD-TYPE    106     69     61
D6V5, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3             106
  CLUS_2             2              69
  CLUS_3             1              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  EOMES MUTATED        1      0      1      1      1      1      1
  EOMES WILD-TYPE     41     23     46     45     25     24     32
D6V6, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              23
  CLUS_3             1              46
  CLUS_4             1              45
  CLUS_5             1              25
  CLUS_6             1              24
  CLUS_7             1              32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  EOMES MUTATED        4      1      1
  EOMES WILD-TYPE     98     48     91
D6V7, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             4              98
  CLUS_2             1              48
  CLUS_3             1              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EOMES MUTATED        3      0      2      1
  EOMES WILD-TYPE     73     50     93     21
D6V8, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3              73
  CLUS_2             0              50
  CLUS_3             2              93
  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
  EOMES MUTATED        3      2      1
  EOMES WILD-TYPE     76     58     45
D6V9, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3              76
  CLUS_2             2              58
  CLUS_3             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  EOMES MUTATED        0      1      1      0      1      1      1      1
  EOMES WILD-TYPE     24     28     32     24     10     20     20     21
D6V10, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             0              24
  CLUS_2             1              28
  CLUS_3             1              32
  CLUS_4             0              24
  CLUS_5             1              10
  CLUS_6             1              20
  CLUS_7             1              20
  CLUS_8             1              21
[1] 8 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 = PKD2 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PKD2 MUTATED        1      2      3      0
  PKD2 WILD-TYPE     61     81     67     25
D7V1, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            1             61
  CLUS_2            2             81
  CLUS_3            3             67
  CLUS_4            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PKD2 MUTATED        0      2      2      1      1      0      0
  PKD2 WILD-TYPE     45     44     55     34     44     13      3
D7V2, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            0             45
  CLUS_2            2             44
  CLUS_3            2             55
  CLUS_4            1             34
  CLUS_5            1             44
  CLUS_6            0             13
  CLUS_7            0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PKD2 MUTATED        1      1      1      1
  PKD2 WILD-TYPE     54     41     53     55
D7V3, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            1             54
  CLUS_2            1             41
  CLUS_3            1             53
  CLUS_4            1             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PKD2 MUTATED        1      0      2      1      0      0
  PKD2 WILD-TYPE     24     34     44     60     19     22
D7V4, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            1             24
  CLUS_2            0             34
  CLUS_3            2             44
  CLUS_4            1             60
  CLUS_5            0             19
  CLUS_6            0             22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PKD2 MUTATED        3      2      1
  PKD2 WILD-TYPE    106     69     61
D7V5, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            3            106
  CLUS_2            2             69
  CLUS_3            1             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PKD2 MUTATED        0      1      2      1      2      0      0
  PKD2 WILD-TYPE     42     22     45     45     24     25     33
D7V6, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            1             22
  CLUS_3            2             45
  CLUS_4            1             45
  CLUS_5            2             24
  CLUS_6            0             25
  CLUS_7            0             33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PKD2 MUTATED        1      2      3
  PKD2 WILD-TYPE    101     47     89
D7V7, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            1            101
  CLUS_2            2             47
  CLUS_3            3             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PKD2 MUTATED        0      2      3      1
  PKD2 WILD-TYPE     76     48     92     21
D7V8, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            0             76
  CLUS_2            2             48
  CLUS_3            3             92
  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
  PKD2 MUTATED        1      1      3
  PKD2 WILD-TYPE     78     59     43
D7V9, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            1             78
  CLUS_2            1             59
  CLUS_3            3             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PKD2 MUTATED        0      0      1      2      0      0      1      1
  PKD2 WILD-TYPE     24     29     32     22     11     21     20     21
D7V10, multiclass
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  CLUS_1            0             24
  CLUS_2            0             29
  CLUS_3            1             32
  CLUS_4            2             22
  CLUS_5            0             11
  CLUS_6            0             21
  CLUS_7            1             20
  CLUS_8            1             21
[1] 8 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 = LTBP3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LTBP3 MUTATED        0      1      4      0
  LTBP3 WILD-TYPE     62     82     66     25
D8V1, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              62
  CLUS_2             1              82
  CLUS_3             4              66
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LTBP3 MUTATED        0      1      3      0      1      0      0
  LTBP3 WILD-TYPE     45     45     54     35     44     13      3
D8V2, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              45
  CLUS_2             1              45
  CLUS_3             3              54
  CLUS_4             0              35
  CLUS_5             1              44
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LTBP3 MUTATED        0      1      0      2
  LTBP3 WILD-TYPE     55     41     54     54
D8V3, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              55
  CLUS_2             1              41
  CLUS_3             0              54
  CLUS_4             2              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LTBP3 MUTATED        0      0      2      1      0      0
  LTBP3 WILD-TYPE     25     34     44     60     19     22
D8V4, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              25
  CLUS_2             0              34
  CLUS_3             2              44
  CLUS_4             1              60
  CLUS_5             0              19
  CLUS_6             0              22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LTBP3 MUTATED        2      3      0
  LTBP3 WILD-TYPE    107     68     62
D8V5, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             2             107
  CLUS_2             3              68
  CLUS_3             0              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LTBP3 MUTATED        0      0      2      0      2      1      0
  LTBP3 WILD-TYPE     42     23     45     46     24     24     33
D8V6, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              23
  CLUS_3             2              45
  CLUS_4             0              46
  CLUS_5             2              24
  CLUS_6             1              24
  CLUS_7             0              33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LTBP3 MUTATED        0      1      4
  LTBP3 WILD-TYPE    102     48     88
D8V7, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0             102
  CLUS_2             1              48
  CLUS_3             4              88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LTBP3 MUTATED        0      0      5      0
  LTBP3 WILD-TYPE     76     50     90     22
D8V8, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              76
  CLUS_2             0              50
  CLUS_3             5              90
  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
  LTBP3 MUTATED        0      3      1
  LTBP3 WILD-TYPE     79     57     45
D8V9, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              79
  CLUS_2             3              57
  CLUS_3             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LTBP3 MUTATED        0      0      3      1      0      0      0      0
  LTBP3 WILD-TYPE     24     29     30     23     11     21     21     22
D8V10, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              24
  CLUS_2             0              29
  CLUS_3             3              30
  CLUS_4             1              23
  CLUS_5             0              11
  CLUS_6             0              21
  CLUS_7             0              21
  CLUS_8             0              22
[1] 8 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 = SHROOM4 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        2      1      4      1
  SHROOM4 WILD-TYPE     60     82     66     24
D9V1, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               2                60
  CLUS_2               1                82
  CLUS_3               4                66
  CLUS_4               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SHROOM4 MUTATED        1      2      3      0      1      1      0
  SHROOM4 WILD-TYPE     44     44     54     35     44     12      3
D9V2, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                44
  CLUS_2               2                44
  CLUS_3               3                54
  CLUS_4               0                35
  CLUS_5               1                44
  CLUS_6               1                12
  CLUS_7               0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        1      2      4      1
  SHROOM4 WILD-TYPE     54     40     50     55
D9V3, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                54
  CLUS_2               2                40
  CLUS_3               4                50
  CLUS_4               1                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  SHROOM4 MUTATED        1      0      3      4      0      0
  SHROOM4 WILD-TYPE     24     34     43     57     19     22
D9V4, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                24
  CLUS_2               0                34
  CLUS_3               3                43
  CLUS_4               4                57
  CLUS_5               0                19
  CLUS_6               0                22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        3      4      1
  SHROOM4 WILD-TYPE    106     67     61
D9V5, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               3               106
  CLUS_2               4                67
  CLUS_3               1                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  SHROOM4 MUTATED        1      0      3      1      1      1      1
  SHROOM4 WILD-TYPE     41     23     44     45     25     24     32
D9V6, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               0                23
  CLUS_3               3                44
  CLUS_4               1                45
  CLUS_5               1                25
  CLUS_6               1                24
  CLUS_7               1                32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SHROOM4 MUTATED        2      1      5
  SHROOM4 WILD-TYPE    100     48     87
D9V7, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               2               100
  CLUS_2               1                48
  CLUS_3               5                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SHROOM4 MUTATED        3      0      5      0
  SHROOM4 WILD-TYPE     73     50     90     22
D9V8, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               3                73
  CLUS_2               0                50
  CLUS_3               5                90
  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
  SHROOM4 MUTATED        2      2      2
  SHROOM4 WILD-TYPE     77     58     44
D9V9, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               2                77
  CLUS_2               2                58
  CLUS_3               2                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  SHROOM4 MUTATED        0      1      1      1      1      1      1      0
  SHROOM4 WILD-TYPE     24     28     32     23     10     20     20     22
D9V10, multiclass
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  CLUS_1               0                24
  CLUS_2               1                28
  CLUS_3               1                32
  CLUS_4               1                23
  CLUS_5               1                10
  CLUS_6               1                20
  CLUS_7               1                20
  CLUS_8               0                22
[1] 8 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 = WNK1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WNK1 MUTATED        0      4      2      0
  WNK1 WILD-TYPE     62     79     68     25
D10V1, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            0             62
  CLUS_2            4             79
  CLUS_3            2             68
  CLUS_4            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  WNK1 MUTATED        1      2      2      1      0      0      0
  WNK1 WILD-TYPE     44     44     55     34     45     13      3
D10V2, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            1             44
  CLUS_2            2             44
  CLUS_3            2             55
  CLUS_4            1             34
  CLUS_5            0             45
  CLUS_6            0             13
  CLUS_7            0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WNK1 MUTATED        0      1      3      2
  WNK1 WILD-TYPE     55     41     51     54
D10V3, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            0             55
  CLUS_2            1             41
  CLUS_3            3             51
  CLUS_4            2             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  WNK1 MUTATED        0      0      2      2      1      1
  WNK1 WILD-TYPE     25     34     44     59     18     21
D10V4, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            0             25
  CLUS_2            0             34
  CLUS_3            2             44
  CLUS_4            2             59
  CLUS_5            1             18
  CLUS_6            1             21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  WNK1 MUTATED        2      2      2
  WNK1 WILD-TYPE    107     69     60
D10V5, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            2            107
  CLUS_2            2             69
  CLUS_3            2             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  WNK1 MUTATED        1      0      2      2      1      0      0
  WNK1 WILD-TYPE     41     23     45     44     25     25     33
D10V6, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            0             23
  CLUS_3            2             45
  CLUS_4            2             44
  CLUS_5            1             25
  CLUS_6            0             25
  CLUS_7            0             33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  WNK1 MUTATED        2      1      3
  WNK1 WILD-TYPE    100     48     89
D10V7, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            2            100
  CLUS_2            1             48
  CLUS_3            3             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  WNK1 MUTATED        1      1      3      1
  WNK1 WILD-TYPE     75     49     92     21
D10V8, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            1             75
  CLUS_2            1             49
  CLUS_3            3             92
  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
  WNK1 MUTATED        2      1      1
  WNK1 WILD-TYPE     77     59     45
D10V9, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            2             77
  CLUS_2            1             59
  CLUS_3            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  WNK1 MUTATED        0      1      1      1      0      0      0      1
  WNK1 WILD-TYPE     24     28     32     23     11     21     21     21
D10V10, multiclass
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  CLUS_1            0             24
  CLUS_2            1             28
  CLUS_3            1             32
  CLUS_4            1             23
  CLUS_5            0             11
  CLUS_6            0             21
  CLUS_7            0             21
  CLUS_8            1             21
[1] 8 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 = ANP32E MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ANP32E MUTATED        2      1      1      0
  ANP32E WILD-TYPE     60     82     69     25
D11V1, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              2               60
  CLUS_2              1               82
  CLUS_3              1               69
  CLUS_4              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ANP32E MUTATED        0      1      1      0      0      2      0
  ANP32E WILD-TYPE     45     45     56     35     45     11      3
D11V2, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              0               45
  CLUS_2              1               45
  CLUS_3              1               56
  CLUS_4              0               35
  CLUS_5              0               45
  CLUS_6              2               11
  CLUS_7              0                3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ANP32E MUTATED        0      0      2      1
  ANP32E WILD-TYPE     55     42     52     55
D11V3, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              0               55
  CLUS_2              0               42
  CLUS_3              2               52
  CLUS_4              1               55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ANP32E MUTATED        0      0      1      2      0      0
  ANP32E WILD-TYPE     25     34     45     59     19     22
D11V4, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              0               25
  CLUS_2              0               34
  CLUS_3              1               45
  CLUS_4              2               59
  CLUS_5              0               19
  CLUS_6              0               22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ANP32E MUTATED        1      3      0
  ANP32E WILD-TYPE    108     68     62
D11V5, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              1              108
  CLUS_2              3               68
  CLUS_3              0               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ANP32E MUTATED        1      0      1      0      0      2      0
  ANP32E WILD-TYPE     41     23     46     46     26     23     33
D11V6, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              1               41
  CLUS_2              0               23
  CLUS_3              1               46
  CLUS_4              0               46
  CLUS_5              0               26
  CLUS_6              2               23
  CLUS_7              0               33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ANP32E MUTATED        0      1      3
  ANP32E WILD-TYPE    102     48     89
D11V7, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              0              102
  CLUS_2              1               48
  CLUS_3              3               89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ANP32E MUTATED        0      1      3      0
  ANP32E WILD-TYPE     76     49     92     22
D11V8, multiclass
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  CLUS_1              0               76
  CLUS_2              1               49
  CLUS_3              3               92
  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
  ANP32E MUTATED        0      0      1
  ANP32E WILD-TYPE     79     60     45
D11V9, multiclass
[1] "Remove cluster labels:" "ANP32E MUTATED"        
clus
  ANP32E MUTATED ANP32E WILD-TYPE 
               1              184 
      TCGA-3B-A9HI       TCGA-3B-A9HL       TCGA-3B-A9HP       TCGA-3B-A9HQ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-3B-A9HR       TCGA-3B-A9HS       TCGA-3B-A9HU       TCGA-3B-A9HX 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-3B-A9HY       TCGA-3B-A9HZ       TCGA-3B-A9I1       TCGA-3B-A9I3 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-3R-A8YX       TCGA-DX-A1KU       TCGA-DX-A1KW       TCGA-DX-A1KX 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A1KY       TCGA-DX-A1KZ       TCGA-DX-A1L0       TCGA-DX-A23R 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A23T       TCGA-DX-A23V       TCGA-DX-A240       TCGA-DX-A2IZ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A2J0       TCGA-DX-A2J1       TCGA-DX-A3LS       TCGA-DX-A3LW 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A3LY       TCGA-DX-A3M1       TCGA-DX-A3M2       TCGA-DX-A3U5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A3U6       TCGA-DX-A3U7       TCGA-DX-A3U8       TCGA-DX-A3U9 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A3UA       TCGA-DX-A48K       TCGA-DX-A48L       TCGA-DX-A48N 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A48O       TCGA-DX-A6BA       TCGA-DX-A6BB       TCGA-DX-A6BE 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A6BF       TCGA-DX-A6YQ       TCGA-DX-A6YR       TCGA-DX-A6YU 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A6YX       TCGA-DX-A6YZ       TCGA-DX-A7EI       TCGA-DX-A7EQ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A7ES       TCGA-DX-A7ET       TCGA-DX-A7EU       TCGA-DX-A8BG 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BH       TCGA-DX-A8BJ       TCGA-DX-A8BK       TCGA-DX-A8BL 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BM       TCGA-DX-A8BN       TCGA-DX-A8BO       TCGA-DX-A8BP 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BQ       TCGA-DX-A8BR       TCGA-DX-A8BS       TCGA-DX-A8BT 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BU       TCGA-DX-A8BV       TCGA-DX-A8BX       TCGA-DX-AATS 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2F       TCGA-DX-AB2G       TCGA-DX-AB2H       TCGA-DX-AB2J 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2O       TCGA-DX-AB2P       TCGA-DX-AB2Q       TCGA-DX-AB2S 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2T       TCGA-DX-AB2V       TCGA-DX-AB2W       TCGA-DX-AB2X 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2Z       TCGA-DX-AB30       TCGA-DX-AB32       TCGA-DX-AB35 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB36       TCGA-DX-AB37       TCGA-DX-AB3A       TCGA-DX-AB3B 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB3C       TCGA-FX-A2QS       TCGA-FX-A3NJ       TCGA-FX-A3NK 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-FX-A3RE       TCGA-FX-A3TO       TCGA-FX-A76Y       TCGA-FX-A8OO 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-HB-A2OT       TCGA-HB-A3YV       TCGA-HB-A43Z       TCGA-HB-A5W3 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-HS-A5N7       TCGA-HS-A5N8       TCGA-IE-A3OV       TCGA-IE-A4EH 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-IE-A4EI       TCGA-IE-A4EJ       TCGA-IF-A4AJ       TCGA-IF-A4AK 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-IS-A3K7       TCGA-IS-A3KA       TCGA-IW-A3M4       TCGA-IW-A3M5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-IW-A3M6       TCGA-JV-A5VE       TCGA-JV-A5VF       TCGA-JV-A75J 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-K1-A3PO       TCGA-K1-A6RT       TCGA-K1-A6RU       TCGA-K1-A6RV 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-KD-A5QS       TCGA-KD-A5QT       TCGA-KD-A5QU       TCGA-KF-A41W 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-LI-A67I       TCGA-LI-A9QH       TCGA-MB-A5Y8       TCGA-MB-A5Y9 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-MB-A5YA       TCGA-MB-A8JK       TCGA-MB-A8JL       TCGA-MJ-A68H 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-MJ-A850       TCGA-MO-A47R       TCGA-PC-A5DK       TCGA-PC-A5DN 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-PC-A5DO       TCGA-PT-A8TR       TCGA-QC-A6FX       TCGA-QC-A7B5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-QC-AA9N       TCGA-QQ-A5VB       TCGA-QQ-A5VC       TCGA-QQ-A5VD 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-QQ-A8VD       TCGA-QQ-A8VG       TCGA-QQ-A8VH       TCGA-RN-AAAQ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-SG-A6Z4       TCGA-SG-A6Z7       TCGA-SG-A849       TCGA-SI-A71O 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-SI-A71P       TCGA-SI-A71Q       TCGA-SI-AA8B       TCGA-SI-AA8C 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-VT-AB3D       TCGA-WK-A8XO       TCGA-WK-A8XQ       TCGA-WK-A8XS 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-WK-A8XT       TCGA-WK-A8XX       TCGA-WK-A8XY       TCGA-WK-A8XZ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-WK-A8Y0       TCGA-WP-A9GB       TCGA-X2-A95T       TCGA-X6-A7W8 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-X6-A7WC       TCGA-X6-A8C2       TCGA-X6-A8C3       TCGA-X6-A8C5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-X6-A8C6       TCGA-X6-A8C7       TCGA-X9-A971       TCGA-X9-A973 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-Z4-A8JB       TCGA-Z4-A9VC       TCGA-Z4-AAPF       TCGA-Z4-AAPG 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ANP32E MUTATED        0      0      0      0      0      0      1      0
  ANP32E WILD-TYPE     24     29     33     24     11     21     20     22
D11V10, multiclass
[1] "Remove cluster labels:" "ANP32E MUTATED"        
clus
  ANP32E MUTATED ANP32E WILD-TYPE 
               1              184 
      TCGA-3B-A9HI       TCGA-3B-A9HL       TCGA-3B-A9HP       TCGA-3B-A9HQ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-3B-A9HR       TCGA-3B-A9HS       TCGA-3B-A9HU       TCGA-3B-A9HX 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-3B-A9HY       TCGA-3B-A9HZ       TCGA-3B-A9I1       TCGA-3B-A9I3 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-3R-A8YX       TCGA-DX-A1KU       TCGA-DX-A1KW       TCGA-DX-A1KX 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A1KY       TCGA-DX-A1KZ       TCGA-DX-A1L0       TCGA-DX-A23R 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A23T       TCGA-DX-A23V       TCGA-DX-A240       TCGA-DX-A2IZ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A2J0       TCGA-DX-A2J1       TCGA-DX-A3LS       TCGA-DX-A3LW 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A3LY       TCGA-DX-A3M1       TCGA-DX-A3M2       TCGA-DX-A3U5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A3U6       TCGA-DX-A3U7       TCGA-DX-A3U8       TCGA-DX-A3U9 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A3UA       TCGA-DX-A48K       TCGA-DX-A48L       TCGA-DX-A48N 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A48O       TCGA-DX-A6BA       TCGA-DX-A6BB       TCGA-DX-A6BE 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A6BF       TCGA-DX-A6YQ       TCGA-DX-A6YR       TCGA-DX-A6YU 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A6YX       TCGA-DX-A6YZ       TCGA-DX-A7EI       TCGA-DX-A7EQ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A7ES       TCGA-DX-A7ET       TCGA-DX-A7EU       TCGA-DX-A8BG 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BH       TCGA-DX-A8BJ       TCGA-DX-A8BK       TCGA-DX-A8BL 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BM       TCGA-DX-A8BN       TCGA-DX-A8BO       TCGA-DX-A8BP 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BQ       TCGA-DX-A8BR       TCGA-DX-A8BS       TCGA-DX-A8BT 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-A8BU       TCGA-DX-A8BV       TCGA-DX-A8BX       TCGA-DX-AATS 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2F       TCGA-DX-AB2G       TCGA-DX-AB2H       TCGA-DX-AB2J 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2O       TCGA-DX-AB2P       TCGA-DX-AB2Q       TCGA-DX-AB2S 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2T       TCGA-DX-AB2V       TCGA-DX-AB2W       TCGA-DX-AB2X 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB2Z       TCGA-DX-AB30       TCGA-DX-AB32       TCGA-DX-AB35 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB36       TCGA-DX-AB37       TCGA-DX-AB3A       TCGA-DX-AB3B 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-DX-AB3C       TCGA-FX-A2QS       TCGA-FX-A3NJ       TCGA-FX-A3NK 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-FX-A3RE       TCGA-FX-A3TO       TCGA-FX-A76Y       TCGA-FX-A8OO 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-HB-A2OT       TCGA-HB-A3YV       TCGA-HB-A43Z       TCGA-HB-A5W3 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-HS-A5N7       TCGA-HS-A5N8       TCGA-IE-A3OV       TCGA-IE-A4EH 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-IE-A4EI       TCGA-IE-A4EJ       TCGA-IF-A4AJ       TCGA-IF-A4AK 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-IS-A3K7       TCGA-IS-A3KA       TCGA-IW-A3M4       TCGA-IW-A3M5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-IW-A3M6       TCGA-JV-A5VE       TCGA-JV-A5VF       TCGA-JV-A75J 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-K1-A3PO       TCGA-K1-A6RT       TCGA-K1-A6RU       TCGA-K1-A6RV 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-KD-A5QS       TCGA-KD-A5QT       TCGA-KD-A5QU       TCGA-KF-A41W 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-LI-A67I       TCGA-LI-A9QH       TCGA-MB-A5Y8       TCGA-MB-A5Y9 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-MB-A5YA       TCGA-MB-A8JK       TCGA-MB-A8JL       TCGA-MJ-A68H 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-MJ-A850       TCGA-MO-A47R       TCGA-PC-A5DK       TCGA-PC-A5DN 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-PC-A5DO       TCGA-PT-A8TR       TCGA-QC-A6FX       TCGA-QC-A7B5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-QC-AA9N       TCGA-QQ-A5VB       TCGA-QQ-A5VC       TCGA-QQ-A5VD 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-QQ-A8VD       TCGA-QQ-A8VG       TCGA-QQ-A8VH       TCGA-RN-AAAQ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-SG-A6Z4       TCGA-SG-A6Z7       TCGA-SG-A849       TCGA-SI-A71O 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-SI-A71P       TCGA-SI-A71Q       TCGA-SI-AA8B       TCGA-SI-AA8C 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-VT-AB3D       TCGA-WK-A8XO       TCGA-WK-A8XQ       TCGA-WK-A8XS 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-WK-A8XT       TCGA-WK-A8XX       TCGA-WK-A8XY       TCGA-WK-A8XZ 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-WK-A8Y0       TCGA-WP-A9GB       TCGA-X2-A95T       TCGA-X6-A7W8 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-X6-A7WC       TCGA-X6-A8C2       TCGA-X6-A8C3       TCGA-X6-A8C5 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-X6-A8C6       TCGA-X6-A8C7       TCGA-X9-A971       TCGA-X9-A973 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 
      TCGA-Z4-A8JB       TCGA-Z4-A9VC       TCGA-Z4-AAPF       TCGA-Z4-AAPG 
"ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" "ANP32E WILD-TYPE" 

Clustering(12) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        3      2      1      1
  PTEN WILD-TYPE     59     81     69     24
D12V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             59
  CLUS_2            2             81
  CLUS_3            1             69
  CLUS_4            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        0      0      4      2      1      0      0
  PTEN WILD-TYPE     45     46     53     33     44     13      3
D12V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             45
  CLUS_2            0             46
  CLUS_3            4             53
  CLUS_4            2             33
  CLUS_5            1             44
  CLUS_6            0             13
  CLUS_7            0              3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        1      1      1      1
  PTEN WILD-TYPE     54     41     53     55
D12V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             54
  CLUS_2            1             41
  CLUS_3            1             53
  CLUS_4            1             55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTEN MUTATED        1      0      1      1      0      1
  PTEN WILD-TYPE     24     34     45     60     19     21
D12V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             24
  CLUS_2            0             34
  CLUS_3            1             45
  CLUS_4            1             60
  CLUS_5            0             19
  CLUS_6            1             21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      4      2
  PTEN WILD-TYPE    108     67     60
D12V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1            108
  CLUS_2            4             67
  CLUS_3            2             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTEN MUTATED        0      0      4      2      0      0      1
  PTEN WILD-TYPE     42     23     43     44     26     25     32
D12V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             42
  CLUS_2            0             23
  CLUS_3            4             43
  CLUS_4            2             44
  CLUS_5            0             26
  CLUS_6            0             25
  CLUS_7            1             32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      1      5
  PTEN WILD-TYPE    101     48     87
D12V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1            101
  CLUS_2            1             48
  CLUS_3            5             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        1      1      5      0
  PTEN WILD-TYPE     75     49     90     22
D12V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             75
  CLUS_2            1             49
  CLUS_3            5             90
  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
  PTEN MUTATED        1      4      1
  PTEN WILD-TYPE     78     56     45
D12V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             78
  CLUS_2            4             56
  CLUS_3            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  PTEN MUTATED        1      0      3      2      0      0      0      0
  PTEN WILD-TYPE     23     29     30     22     11     21     21     22
D12V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             23
  CLUS_2            0             29
  CLUS_3            3             30
  CLUS_4            2             22
  CLUS_5            0             11
  CLUS_6            0             21
  CLUS_7            0             21
  CLUS_8            0             22
[1] 8 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 = KRTAP5-5 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        2      2      2      1
  KRTAP5-5 WILD-TYPE     60     81     68     24
D13V1, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                2                 60
  CLUS_2                2                 81
  CLUS_3                2                 68
  CLUS_4                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KRTAP5-5 MUTATED        3      1      0      3      0      0      0
  KRTAP5-5 WILD-TYPE     42     45     57     32     45     13      3
D13V2, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                 42
  CLUS_2                1                 45
  CLUS_3                0                 57
  CLUS_4                3                 32
  CLUS_5                0                 45
  CLUS_6                0                 13
  CLUS_7                0                  3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        3      2      0      1
  KRTAP5-5 WILD-TYPE     52     40     54     55
D13V3, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                 52
  CLUS_2                2                 40
  CLUS_3                0                 54
  CLUS_4                1                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  KRTAP5-5 MUTATED        1      3      0      0      0      2
  KRTAP5-5 WILD-TYPE     24     31     46     61     19     20
D13V4, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 24
  CLUS_2                3                 31
  CLUS_3                0                 46
  CLUS_4                0                 61
  CLUS_5                0                 19
  CLUS_6                2                 20
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP5-5 MUTATED        3      0      4
  KRTAP5-5 WILD-TYPE    106     71     58
D13V5, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                106
  CLUS_2                0                 71
  CLUS_3                4                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KRTAP5-5 MUTATED        2      1      0      4      0      0      0
  KRTAP5-5 WILD-TYPE     40     22     47     42     26     25     33
D13V6, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                1                 22
  CLUS_3                0                 47
  CLUS_4                4                 42
  CLUS_5                0                 26
  CLUS_6                0                 25
  CLUS_7                0                 33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KRTAP5-5 MUTATED        6      0      1
  KRTAP5-5 WILD-TYPE     96     49     91
D13V7, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                6                 96
  CLUS_2                0                 49
  CLUS_3                1                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        4      0      1      2
  KRTAP5-5 WILD-TYPE     72     50     94     20
D13V8, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                4                 72
  CLUS_2                0                 50
  CLUS_3                1                 94
  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
  KRTAP5-5 MUTATED        6      1      0
  KRTAP5-5 WILD-TYPE     73     59     46
D13V9, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                6                 73
  CLUS_2                1                 59
  CLUS_3                0                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  KRTAP5-5 MUTATED        1      3      0      1      0      0      0      2
  KRTAP5-5 WILD-TYPE     23     26     33     23     11     21     21     20
D13V10, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                3                 26
  CLUS_3                0                 33
  CLUS_4                1                 23
  CLUS_5                0                 11
  CLUS_6                0                 21
  CLUS_7                0                 21
  CLUS_8                2                 20
[1] 8 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 = TRAF7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRAF7 MUTATED        1      2      0      1
  TRAF7 WILD-TYPE     61     81     70     24
D14V1, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             1              61
  CLUS_2             2              81
  CLUS_3             0              70
  CLUS_4             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TRAF7 MUTATED        2      1      0      0      1      0      0
  TRAF7 WILD-TYPE     43     45     57     35     44     13      3
D14V2, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              43
  CLUS_2             1              45
  CLUS_3             0              57
  CLUS_4             0              35
  CLUS_5             1              44
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRAF7 MUTATED        2      1      0      1
  TRAF7 WILD-TYPE     53     41     54     55
D14V3, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              53
  CLUS_2             1              41
  CLUS_3             0              54
  CLUS_4             1              55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  TRAF7 MUTATED        2      1      1      0      0      0
  TRAF7 WILD-TYPE     23     33     45     61     19     22
D14V4, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              23
  CLUS_2             1              33
  CLUS_3             1              45
  CLUS_4             0              61
  CLUS_5             0              19
  CLUS_6             0              22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TRAF7 MUTATED        3      0      1
  TRAF7 WILD-TYPE    106     71     61
D14V5, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             3             106
  CLUS_2             0              71
  CLUS_3             1              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TRAF7 MUTATED        2      0      0      0      0      0      2
  TRAF7 WILD-TYPE     40     23     47     46     26     25     31
D14V6, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             0              23
  CLUS_3             0              47
  CLUS_4             0              46
  CLUS_5             0              26
  CLUS_6             0              25
  CLUS_7             2              31
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TRAF7 MUTATED        2      1      1
  TRAF7 WILD-TYPE    100     48     91
D14V7, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2             100
  CLUS_2             1              48
  CLUS_3             1              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRAF7 MUTATED        1      1      2      0
  TRAF7 WILD-TYPE     75     49     93     22
D14V8, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             1              75
  CLUS_2             1              49
  CLUS_3             2              93
  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
  TRAF7 MUTATED        1      2      0
  TRAF7 WILD-TYPE     78     58     46
D14V9, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             1              78
  CLUS_2             2              58
  CLUS_3             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  TRAF7 MUTATED        0      1      0      2      0      0      0      0
  TRAF7 WILD-TYPE     24     28     33     22     11     21     21     22
D14V10, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             0              24
  CLUS_2             1              28
  CLUS_3             0              33
  CLUS_4             2              22
  CLUS_5             0              11
  CLUS_6             0              21
  CLUS_7             0              21
  CLUS_8             0              22
[1] 8 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 = MEGF9 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEGF9 MUTATED        1      1      1      0
  MEGF9 WILD-TYPE     61     82     69     25
D15V1, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              61
  CLUS_2             1              82
  CLUS_3             1              69
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MEGF9 MUTATED        1      0      1      0      1      0      0
  MEGF9 WILD-TYPE     44     46     56     35     44     13      3
D15V2, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              44
  CLUS_2             0              46
  CLUS_3             1              56
  CLUS_4             0              35
  CLUS_5             1              44
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEGF9 MUTATED        0      0      1      0
  MEGF9 WILD-TYPE     55     42     53     56
D15V3, multiclass
[1] "Remove cluster labels:" "MEGF9 MUTATED"         
clus
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              1             206 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HV 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-3B-A9I1      TCGA-3B-A9I3      TCGA-3R-A8YX      TCGA-DX-A1KU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A1KW      TCGA-DX-A1KX      TCGA-DX-A1KY      TCGA-DX-A1KZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A1L0      TCGA-DX-A1L1      TCGA-DX-A1L2      TCGA-DX-A1L3 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A1L4      TCGA-DX-A23R      TCGA-DX-A23T      TCGA-DX-A23U 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A23V      TCGA-DX-A23Y      TCGA-DX-A240      TCGA-DX-A2IZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A2J4      TCGA-DX-A3LS 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3LT      TCGA-DX-A3LU      TCGA-DX-A3LW      TCGA-DX-A3LY 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5      TCGA-DX-A3U6 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3U7      TCGA-DX-A3U8      TCGA-DX-A3U9      TCGA-DX-A3UA 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3UB      TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3UF      TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A48N      TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A48U      TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6B9      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6YQ      TCGA-DX-A6YU      TCGA-DX-A6YX      TCGA-DX-A6YZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6Z0      TCGA-DX-A6Z2      TCGA-DX-A7EF      TCGA-DX-A7EI 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A7EL      TCGA-DX-A7EM      TCGA-DX-A7EN      TCGA-DX-A7EQ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A7ER      TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BG      TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BL      TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BP      TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BT      TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-A8BX 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BZ      TCGA-DX-AATS      TCGA-DX-AB2E      TCGA-DX-AB2F 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2G      TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3RE      TCGA-FX-A3TO 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-HB-A3L4      TCGA-HB-A3YV      TCGA-HB-A43Z      TCGA-HB-A5W3 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-HS-A5N7      TCGA-HS-A5N8      TCGA-IE-A3OV      TCGA-IE-A4EH 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IE-A4EI      TCGA-IE-A4EJ      TCGA-IE-A4EK      TCGA-IE-A6BZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IS-A3K6      TCGA-IS-A3K7      TCGA-IS-A3K8      TCGA-IS-A3KA 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6      TCGA-JV-A5VE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-JV-A5VF      TCGA-K1-A3PO      TCGA-K1-A42W      TCGA-K1-A42X 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-K1-A6RT      TCGA-K1-A6RU      TCGA-K1-A6RV      TCGA-KF-A41W 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-LI-A67I      TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-MB-A5YA      TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MO-A47R 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-N1-A6IA      TCGA-PC-A5DK      TCGA-PC-A5DL      TCGA-PC-A5DN 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-PC-A5DO      TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-AA9N 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A5V2      TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VG      TCGA-QQ-A8VH 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-RN-A68Q      TCGA-RN-AAAQ      TCGA-SG-A6Z4      TCGA-SG-A6Z7 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P      TCGA-SI-A71Q 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QT      TCGA-UE-A6QU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-VT-A80G      TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A7W8      TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A8C3      TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A8C7      TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-Z4-AAPF      TCGA-Z4-AAPG 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MEGF9 MUTATED        0      0      0      0      0      1
  MEGF9 WILD-TYPE     25     34     46     61     19     21
D15V4, multiclass
[1] "Remove cluster labels:" "MEGF9 MUTATED"         
clus
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              1             206 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HV 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-3B-A9I1      TCGA-3B-A9I3      TCGA-3R-A8YX      TCGA-DX-A1KU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A1KW      TCGA-DX-A1KX      TCGA-DX-A1KY      TCGA-DX-A1KZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A1L0      TCGA-DX-A1L1      TCGA-DX-A1L2      TCGA-DX-A1L3 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A1L4      TCGA-DX-A23R      TCGA-DX-A23T      TCGA-DX-A23U 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A23V      TCGA-DX-A23Y      TCGA-DX-A240      TCGA-DX-A2IZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A2J4      TCGA-DX-A3LS 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3LT      TCGA-DX-A3LU      TCGA-DX-A3LW      TCGA-DX-A3LY 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5      TCGA-DX-A3U6 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3U7      TCGA-DX-A3U8      TCGA-DX-A3U9      TCGA-DX-A3UA 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3UB      TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A3UF      TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A48N      TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A48U      TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6B9      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6YQ      TCGA-DX-A6YU      TCGA-DX-A6YX      TCGA-DX-A6YZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A6Z0      TCGA-DX-A6Z2      TCGA-DX-A7EF      TCGA-DX-A7EI 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A7EL      TCGA-DX-A7EM      TCGA-DX-A7EN      TCGA-DX-A7EQ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A7ER      TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BG      TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BL      TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BP      TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BT      TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-A8BX 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-A8BZ      TCGA-DX-AATS      TCGA-DX-AB2E      TCGA-DX-AB2F 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2G      TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3RE      TCGA-FX-A3TO 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-HB-A3L4      TCGA-HB-A3YV      TCGA-HB-A43Z      TCGA-HB-A5W3 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-HS-A5N7      TCGA-HS-A5N8      TCGA-IE-A3OV      TCGA-IE-A4EH 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IE-A4EI      TCGA-IE-A4EJ      TCGA-IE-A4EK      TCGA-IE-A6BZ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IS-A3K6      TCGA-IS-A3K7      TCGA-IS-A3K8      TCGA-IS-A3KA 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6      TCGA-JV-A5VE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-JV-A5VF      TCGA-K1-A3PO      TCGA-K1-A42W      TCGA-K1-A42X 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-K1-A6RT      TCGA-K1-A6RU      TCGA-K1-A6RV      TCGA-KF-A41W 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-LI-A67I      TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-MB-A5YA      TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MO-A47R 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-N1-A6IA      TCGA-PC-A5DK      TCGA-PC-A5DL      TCGA-PC-A5DN 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-PC-A5DO      TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-AA9N 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A5V2      TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VG      TCGA-QQ-A8VH 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-RN-A68Q      TCGA-RN-AAAQ      TCGA-SG-A6Z4      TCGA-SG-A6Z7 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P      TCGA-SI-A71Q 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QT      TCGA-UE-A6QU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-VT-A80G      TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A7W8      TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A8C3      TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A8C7      TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-Z4-AAPF      TCGA-Z4-AAPG 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MEGF9 MUTATED        2      1      0
  MEGF9 WILD-TYPE    107     70     62
D15V5, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             2             107
  CLUS_2             1              70
  CLUS_3             0              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MEGF9 MUTATED        1      0      1      0      0      0      1
  MEGF9 WILD-TYPE     41     23     46     46     26     25     32
D15V6, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              23
  CLUS_3             1              46
  CLUS_4             0              46
  CLUS_5             0              26
  CLUS_6             0              25
  CLUS_7             1              32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MEGF9 MUTATED        1      1      1
  MEGF9 WILD-TYPE    101     48     91
D15V7, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1             101
  CLUS_2             1              48
  CLUS_3             1              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEGF9 MUTATED        2      0      1      0
  MEGF9 WILD-TYPE     74     50     94     22
D15V8, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             2              74
  CLUS_2             0              50
  CLUS_3             1              94
  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
  MEGF9 MUTATED        1      1      1
  MEGF9 WILD-TYPE     78     59     45
D15V9, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              78
  CLUS_2             1              59
  CLUS_3             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MEGF9 MUTATED        0      1      1      0      0      0      1      0
  MEGF9 WILD-TYPE     24     28     32     24     11     21     20     22
D15V10, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             0              24
  CLUS_2             1              28
  CLUS_3             1              32
  CLUS_4             0              24
  CLUS_5             0              11
  CLUS_6             0              21
  CLUS_7             1              20
  CLUS_8             0              22
[1] 8 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 = LOR MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LOR MUTATED        0      2      1      3
  LOR WILD-TYPE     62     81     69     22
D16V1, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           0            62
  CLUS_2           2            81
  CLUS_3           1            69
  CLUS_4           3            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 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LOR MUTATED        1      2      0      1      1      1      0
  LOR WILD-TYPE     44     44     57     34     44     12      3
D16V2, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           1            44
  CLUS_2           2            44
  CLUS_3           0            57
  CLUS_4           1            34
  CLUS_5           1            44
  CLUS_6           1            12
  CLUS_7           0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LOR MUTATED        4      1      0      0
  LOR WILD-TYPE     51     41     54     56
D16V3, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           4            51
  CLUS_2           1            41
  CLUS_3           0            54
  CLUS_4           0            56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LOR MUTATED        1      3      0      0      0      1
  LOR WILD-TYPE     24     31     46     61     19     21
D16V4, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           1            24
  CLUS_2           3            31
  CLUS_3           0            46
  CLUS_4           0            61
  CLUS_5           0            19
  CLUS_6           1            21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  LOR MUTATED        4      1      1
  LOR WILD-TYPE    105     70     61
D16V5, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           4           105
  CLUS_2           1            70
  CLUS_3           1            61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LOR MUTATED        1      2      0      1      0      1      1
  LOR WILD-TYPE     41     21     47     45     26     24     32
D16V6, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           1            41
  CLUS_2           2            21
  CLUS_3           0            47
  CLUS_4           1            45
  CLUS_5           0            26
  CLUS_6           1            24
  CLUS_7           1            32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  LOR MUTATED        5      0      1
  LOR WILD-TYPE     97     49     91
D16V7, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           5            97
  CLUS_2           0            49
  CLUS_3           1            91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LOR MUTATED        4      0      1      1
  LOR WILD-TYPE     72     50     94     21
D16V8, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           4            72
  CLUS_2           0            50
  CLUS_3           1            94
  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
  LOR MUTATED        1      0      0
  LOR WILD-TYPE     78     60     46
D16V9, multiclass
[1] "Remove cluster labels:" "LOR MUTATED"           
clus
  LOR MUTATED LOR WILD-TYPE 
            1           184 
   TCGA-3B-A9HI    TCGA-3B-A9HL    TCGA-3B-A9HP    TCGA-3B-A9HQ    TCGA-3B-A9HR 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-3B-A9HS    TCGA-3B-A9HU    TCGA-3B-A9HX    TCGA-3B-A9HY    TCGA-3B-A9HZ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-3B-A9I1    TCGA-3B-A9I3    TCGA-3R-A8YX    TCGA-DX-A1KU    TCGA-DX-A1KW 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A1KX    TCGA-DX-A1KY    TCGA-DX-A1KZ    TCGA-DX-A1L0    TCGA-DX-A23R 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A23T    TCGA-DX-A23V    TCGA-DX-A240    TCGA-DX-A2IZ    TCGA-DX-A2J0 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A2J1    TCGA-DX-A3LS    TCGA-DX-A3LW    TCGA-DX-A3LY    TCGA-DX-A3M1 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A3M2    TCGA-DX-A3U5    TCGA-DX-A3U6    TCGA-DX-A3U7    TCGA-DX-A3U8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A3U9    TCGA-DX-A3UA    TCGA-DX-A48K    TCGA-DX-A48L    TCGA-DX-A48N 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A48O    TCGA-DX-A6BA    TCGA-DX-A6BB    TCGA-DX-A6BE    TCGA-DX-A6BF 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A6YQ    TCGA-DX-A6YR    TCGA-DX-A6YU    TCGA-DX-A6YX    TCGA-DX-A6YZ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A7EI    TCGA-DX-A7EQ    TCGA-DX-A7ES    TCGA-DX-A7ET    TCGA-DX-A7EU 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BG    TCGA-DX-A8BH    TCGA-DX-A8BJ    TCGA-DX-A8BK    TCGA-DX-A8BL 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BM    TCGA-DX-A8BN    TCGA-DX-A8BO    TCGA-DX-A8BP    TCGA-DX-A8BQ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BR    TCGA-DX-A8BS    TCGA-DX-A8BT    TCGA-DX-A8BU    TCGA-DX-A8BV 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BX    TCGA-DX-AATS    TCGA-DX-AB2G    TCGA-DX-AB2H    TCGA-DX-AB2J 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB2O    TCGA-DX-AB2P    TCGA-DX-AB2Q    TCGA-DX-AB2S    TCGA-DX-AB2T 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB2V    TCGA-DX-AB2W    TCGA-DX-AB2X    TCGA-DX-AB2Z    TCGA-DX-AB30 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB32    TCGA-DX-AB35    TCGA-DX-AB36    TCGA-DX-AB37    TCGA-DX-AB3A 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB3B    TCGA-DX-AB3C    TCGA-FX-A2QS    TCGA-FX-A3NJ    TCGA-FX-A3NK 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-FX-A3RE    TCGA-FX-A3TO    TCGA-FX-A76Y    TCGA-FX-A8OO    TCGA-HB-A2OT 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-HB-A3YV    TCGA-HB-A43Z    TCGA-HB-A5W3    TCGA-HS-A5N7    TCGA-HS-A5N8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IE-A3OV    TCGA-IE-A4EH    TCGA-IE-A4EI    TCGA-IE-A4EJ    TCGA-IF-A4AJ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IF-A4AK    TCGA-IS-A3K7    TCGA-IS-A3KA    TCGA-IW-A3M4    TCGA-IW-A3M5 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IW-A3M6    TCGA-JV-A5VE    TCGA-JV-A5VF    TCGA-JV-A75J    TCGA-K1-A3PO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-K1-A6RT    TCGA-K1-A6RU    TCGA-K1-A6RV    TCGA-KD-A5QS    TCGA-KD-A5QT 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-KD-A5QU    TCGA-KF-A41W    TCGA-LI-A67I    TCGA-LI-A9QH    TCGA-MB-A5Y8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-MB-A5Y9    TCGA-MB-A5YA    TCGA-MB-A8JK    TCGA-MB-A8JL    TCGA-MJ-A68H 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-MJ-A850    TCGA-MO-A47R    TCGA-PC-A5DK    TCGA-PC-A5DN    TCGA-PC-A5DO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-PT-A8TR    TCGA-QC-A6FX    TCGA-QC-A7B5    TCGA-QC-AA9N    TCGA-QQ-A5VB 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-QQ-A5VC    TCGA-QQ-A5VD    TCGA-QQ-A8VD    TCGA-QQ-A8VG    TCGA-QQ-A8VH 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-RN-AAAQ    TCGA-SG-A6Z4    TCGA-SG-A6Z7    TCGA-SG-A849    TCGA-SI-A71O 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-SI-A71P    TCGA-SI-A71Q    TCGA-SI-AA8B    TCGA-SI-AA8C    TCGA-UE-A6QU 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-VT-AB3D    TCGA-WK-A8XO    TCGA-WK-A8XQ    TCGA-WK-A8XS    TCGA-WK-A8XT 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-WK-A8XX    TCGA-WK-A8XY    TCGA-WK-A8XZ    TCGA-WK-A8Y0    TCGA-WP-A9GB 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X2-A95T    TCGA-X6-A7W8    TCGA-X6-A7WC    TCGA-X6-A8C2    TCGA-X6-A8C3 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X6-A8C5    TCGA-X6-A8C6    TCGA-X6-A8C7    TCGA-X9-A971    TCGA-X9-A973 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-Z4-A8JB    TCGA-Z4-A9VC    TCGA-Z4-AAPF    TCGA-Z4-AAPG 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LOR MUTATED        0      1      0      0      0      0      0      0
  LOR WILD-TYPE     24     28     33     24     11     21     21     22
D16V10, multiclass
[1] "Remove cluster labels:" "LOR MUTATED"           
clus
  LOR MUTATED LOR WILD-TYPE 
            1           184 
   TCGA-3B-A9HI    TCGA-3B-A9HL    TCGA-3B-A9HP    TCGA-3B-A9HQ    TCGA-3B-A9HR 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-3B-A9HS    TCGA-3B-A9HU    TCGA-3B-A9HX    TCGA-3B-A9HY    TCGA-3B-A9HZ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-3B-A9I1    TCGA-3B-A9I3    TCGA-3R-A8YX    TCGA-DX-A1KU    TCGA-DX-A1KW 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A1KX    TCGA-DX-A1KY    TCGA-DX-A1KZ    TCGA-DX-A1L0    TCGA-DX-A23R 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A23T    TCGA-DX-A23V    TCGA-DX-A240    TCGA-DX-A2IZ    TCGA-DX-A2J0 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A2J1    TCGA-DX-A3LS    TCGA-DX-A3LW    TCGA-DX-A3LY    TCGA-DX-A3M1 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A3M2    TCGA-DX-A3U5    TCGA-DX-A3U6    TCGA-DX-A3U7    TCGA-DX-A3U8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A3U9    TCGA-DX-A3UA    TCGA-DX-A48K    TCGA-DX-A48L    TCGA-DX-A48N 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A48O    TCGA-DX-A6BA    TCGA-DX-A6BB    TCGA-DX-A6BE    TCGA-DX-A6BF 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A6YQ    TCGA-DX-A6YR    TCGA-DX-A6YU    TCGA-DX-A6YX    TCGA-DX-A6YZ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A7EI    TCGA-DX-A7EQ    TCGA-DX-A7ES    TCGA-DX-A7ET    TCGA-DX-A7EU 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BG    TCGA-DX-A8BH    TCGA-DX-A8BJ    TCGA-DX-A8BK    TCGA-DX-A8BL 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BM    TCGA-DX-A8BN    TCGA-DX-A8BO    TCGA-DX-A8BP    TCGA-DX-A8BQ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BR    TCGA-DX-A8BS    TCGA-DX-A8BT    TCGA-DX-A8BU    TCGA-DX-A8BV 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-A8BX    TCGA-DX-AATS    TCGA-DX-AB2G    TCGA-DX-AB2H    TCGA-DX-AB2J 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB2O    TCGA-DX-AB2P    TCGA-DX-AB2Q    TCGA-DX-AB2S    TCGA-DX-AB2T 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB2V    TCGA-DX-AB2W    TCGA-DX-AB2X    TCGA-DX-AB2Z    TCGA-DX-AB30 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB32    TCGA-DX-AB35    TCGA-DX-AB36    TCGA-DX-AB37    TCGA-DX-AB3A 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB3B    TCGA-DX-AB3C    TCGA-FX-A2QS    TCGA-FX-A3NJ    TCGA-FX-A3NK 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-FX-A3RE    TCGA-FX-A3TO    TCGA-FX-A76Y    TCGA-FX-A8OO    TCGA-HB-A2OT 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-HB-A3YV    TCGA-HB-A43Z    TCGA-HB-A5W3    TCGA-HS-A5N7    TCGA-HS-A5N8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IE-A3OV    TCGA-IE-A4EH    TCGA-IE-A4EI    TCGA-IE-A4EJ    TCGA-IF-A4AJ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IF-A4AK    TCGA-IS-A3K7    TCGA-IS-A3KA    TCGA-IW-A3M4    TCGA-IW-A3M5 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IW-A3M6    TCGA-JV-A5VE    TCGA-JV-A5VF    TCGA-JV-A75J    TCGA-K1-A3PO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-K1-A6RT    TCGA-K1-A6RU    TCGA-K1-A6RV    TCGA-KD-A5QS    TCGA-KD-A5QT 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-KD-A5QU    TCGA-KF-A41W    TCGA-LI-A67I    TCGA-LI-A9QH    TCGA-MB-A5Y8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-MB-A5Y9    TCGA-MB-A5YA    TCGA-MB-A8JK    TCGA-MB-A8JL    TCGA-MJ-A68H 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-MJ-A850    TCGA-MO-A47R    TCGA-PC-A5DK    TCGA-PC-A5DN    TCGA-PC-A5DO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-PT-A8TR    TCGA-QC-A6FX    TCGA-QC-A7B5    TCGA-QC-AA9N    TCGA-QQ-A5VB 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-QQ-A5VC    TCGA-QQ-A5VD    TCGA-QQ-A8VD    TCGA-QQ-A8VG    TCGA-QQ-A8VH 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-RN-AAAQ    TCGA-SG-A6Z4    TCGA-SG-A6Z7    TCGA-SG-A849    TCGA-SI-A71O 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-SI-A71P    TCGA-SI-A71Q    TCGA-SI-AA8B    TCGA-SI-AA8C    TCGA-UE-A6QU 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-VT-AB3D    TCGA-WK-A8XO    TCGA-WK-A8XQ    TCGA-WK-A8XS    TCGA-WK-A8XT 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-WK-A8XX    TCGA-WK-A8XY    TCGA-WK-A8XZ    TCGA-WK-A8Y0    TCGA-WP-A9GB 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X2-A95T    TCGA-X6-A7W8    TCGA-X6-A7WC    TCGA-X6-A8C2    TCGA-X6-A8C3 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X6-A8C5    TCGA-X6-A8C6    TCGA-X6-A8C7    TCGA-X9-A971    TCGA-X9-A973 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-Z4-A8JB    TCGA-Z4-A9VC    TCGA-Z4-AAPF    TCGA-Z4-AAPG 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 

Clustering(17) Variable = CABLES1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CABLES1 MUTATED        1      1      1      0
  CABLES1 WILD-TYPE     61     82     69     25
D17V1, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                61
  CLUS_2               1                82
  CLUS_3               1                69
  CLUS_4               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CABLES1 MUTATED        1      0      1      0      0      1      0
  CABLES1 WILD-TYPE     44     46     56     35     45     12      3
D17V2, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                44
  CLUS_2               0                46
  CLUS_3               1                56
  CLUS_4               0                35
  CLUS_5               0                45
  CLUS_6               1                12
  CLUS_7               0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CABLES1 MUTATED        1      0      2      0
  CABLES1 WILD-TYPE     54     42     52     56
D17V3, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                54
  CLUS_2               0                42
  CLUS_3               2                52
  CLUS_4               0                56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CABLES1 MUTATED        1      0      0      2      0      0
  CABLES1 WILD-TYPE     24     34     46     59     19     22
D17V4, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                24
  CLUS_2               0                34
  CLUS_3               0                46
  CLUS_4               2                59
  CLUS_5               0                19
  CLUS_6               0                22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CABLES1 MUTATED        0      2      1
  CABLES1 WILD-TYPE    109     69     61
D17V5, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               0               109
  CLUS_2               2                69
  CLUS_3               1                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CABLES1 MUTATED        0      0      1      1      0      1      0
  CABLES1 WILD-TYPE     42     23     46     45     26     24     33
D17V6, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               0                42
  CLUS_2               0                23
  CLUS_3               1                46
  CLUS_4               1                45
  CLUS_5               0                26
  CLUS_6               1                24
  CLUS_7               0                33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CABLES1 MUTATED        1      0      2
  CABLES1 WILD-TYPE    101     49     90
D17V7, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1               101
  CLUS_2               0                49
  CLUS_3               2                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CABLES1 MUTATED        1      0      2      0
  CABLES1 WILD-TYPE     75     50     93     22
D17V8, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                75
  CLUS_2               0                50
  CLUS_3               2                93
  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
  CABLES1 MUTATED        1      1      0
  CABLES1 WILD-TYPE     78     59     46
D17V9, multiclass
[1] "Remove cluster labels:" "CABLES1 MUTATED"       
clus
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                2               183 
       TCGA-3B-A9HI        TCGA-3B-A9HL        TCGA-3B-A9HP        TCGA-3B-A9HQ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-3B-A9HR        TCGA-3B-A9HS        TCGA-3B-A9HU        TCGA-3B-A9HX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-3B-A9HY        TCGA-3B-A9HZ        TCGA-3B-A9I1        TCGA-3B-A9I3 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-3R-A8YX        TCGA-DX-A1KU        TCGA-DX-A1KW        TCGA-DX-A1KX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A1KY        TCGA-DX-A1KZ        TCGA-DX-A1L0        TCGA-DX-A23R 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A23T        TCGA-DX-A23V        TCGA-DX-A240        TCGA-DX-A2IZ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A3LS        TCGA-DX-A3LW 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A3LY        TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A3U6        TCGA-DX-A3U7        TCGA-DX-A3U8        TCGA-DX-A3U9 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A3UA        TCGA-DX-A48K        TCGA-DX-A48N        TCGA-DX-A48O 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A6BA        TCGA-DX-A6BB        TCGA-DX-A6BE        TCGA-DX-A6BF 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A6YQ        TCGA-DX-A6YR        TCGA-DX-A6YU        TCGA-DX-A6YX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A6YZ        TCGA-DX-A7EI        TCGA-DX-A7EQ        TCGA-DX-A7ES 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A7ET        TCGA-DX-A7EU        TCGA-DX-A8BG        TCGA-DX-A8BH 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BJ        TCGA-DX-A8BK        TCGA-DX-A8BL        TCGA-DX-A8BM 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BN        TCGA-DX-A8BO        TCGA-DX-A8BP        TCGA-DX-A8BQ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BR        TCGA-DX-A8BS        TCGA-DX-A8BT        TCGA-DX-A8BU 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BV        TCGA-DX-A8BX        TCGA-DX-AATS        TCGA-DX-AB2F 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2G        TCGA-DX-AB2H        TCGA-DX-AB2J        TCGA-DX-AB2O 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2P        TCGA-DX-AB2Q        TCGA-DX-AB2S        TCGA-DX-AB2T 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2V        TCGA-DX-AB2W        TCGA-DX-AB2X        TCGA-DX-AB2Z 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB30        TCGA-DX-AB32        TCGA-DX-AB35        TCGA-DX-AB36 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB37        TCGA-DX-AB3B        TCGA-DX-AB3C        TCGA-FX-A2QS 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A76Y        TCGA-FX-A8OO        TCGA-HB-A2OT        TCGA-HB-A3YV 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-HB-A43Z        TCGA-HB-A5W3        TCGA-HS-A5N7        TCGA-HS-A5N8 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IE-A4EH        TCGA-IE-A4EI        TCGA-IE-A4EJ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IF-A4AJ        TCGA-IF-A4AK        TCGA-IS-A3K7        TCGA-IS-A3KA 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IW-A3M4        TCGA-IW-A3M5        TCGA-IW-A3M6        TCGA-JV-A5VE 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-JV-A5VF        TCGA-JV-A75J        TCGA-K1-A3PO        TCGA-K1-A6RT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-K1-A6RU        TCGA-K1-A6RV        TCGA-KD-A5QS        TCGA-KD-A5QT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-KD-A5QU        TCGA-KF-A41W        TCGA-LI-A67I        TCGA-LI-A9QH 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MB-A5Y8        TCGA-MB-A5Y9        TCGA-MB-A5YA        TCGA-MB-A8JK 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MB-A8JL        TCGA-MJ-A68H        TCGA-MJ-A850        TCGA-MO-A47R 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-PC-A5DK        TCGA-PC-A5DN        TCGA-PC-A5DO        TCGA-PT-A8TR 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QC-A6FX        TCGA-QC-A7B5        TCGA-QC-AA9N        TCGA-QQ-A5VB 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QQ-A5VC        TCGA-QQ-A5VD        TCGA-QQ-A8VD        TCGA-QQ-A8VG 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QQ-A8VH        TCGA-RN-AAAQ        TCGA-SG-A6Z4        TCGA-SG-A6Z7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SG-A849        TCGA-SI-A71O        TCGA-SI-A71P        TCGA-SI-A71Q 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SI-AA8B        TCGA-SI-AA8C        TCGA-UE-A6QU        TCGA-VT-AB3D 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XO        TCGA-WK-A8XQ        TCGA-WK-A8XS        TCGA-WK-A8XT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XX        TCGA-WK-A8XY        TCGA-WK-A8XZ        TCGA-WK-A8Y0 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WP-A9GB        TCGA-X2-A95T        TCGA-X6-A7W8        TCGA-X6-A7WC 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X6-A8C2        TCGA-X6-A8C3        TCGA-X6-A8C5        TCGA-X6-A8C6 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X6-A8C7        TCGA-X9-A971        TCGA-X9-A973        TCGA-Z4-A8JB 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-Z4-A9VC        TCGA-Z4-AAPF        TCGA-Z4-AAPG 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  CABLES1 MUTATED        0      1      1      0      0      0      0      0
  CABLES1 WILD-TYPE     24     28     32     24     11     21     21     22
D17V10, multiclass
[1] "Remove cluster labels:" "CABLES1 MUTATED"       
clus
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                2               183 
       TCGA-3B-A9HI        TCGA-3B-A9HL        TCGA-3B-A9HP        TCGA-3B-A9HQ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-3B-A9HR        TCGA-3B-A9HS        TCGA-3B-A9HU        TCGA-3B-A9HX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-3B-A9HY        TCGA-3B-A9HZ        TCGA-3B-A9I1        TCGA-3B-A9I3 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-3R-A8YX        TCGA-DX-A1KU        TCGA-DX-A1KW        TCGA-DX-A1KX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A1KY        TCGA-DX-A1KZ        TCGA-DX-A1L0        TCGA-DX-A23R 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A23T        TCGA-DX-A23V        TCGA-DX-A240        TCGA-DX-A2IZ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A3LS        TCGA-DX-A3LW 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A3LY        TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A3U6        TCGA-DX-A3U7        TCGA-DX-A3U8        TCGA-DX-A3U9 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A3UA        TCGA-DX-A48K        TCGA-DX-A48N        TCGA-DX-A48O 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A6BA        TCGA-DX-A6BB        TCGA-DX-A6BE        TCGA-DX-A6BF 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A6YQ        TCGA-DX-A6YR        TCGA-DX-A6YU        TCGA-DX-A6YX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A6YZ        TCGA-DX-A7EI        TCGA-DX-A7EQ        TCGA-DX-A7ES 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A7ET        TCGA-DX-A7EU        TCGA-DX-A8BG        TCGA-DX-A8BH 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BJ        TCGA-DX-A8BK        TCGA-DX-A8BL        TCGA-DX-A8BM 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BN        TCGA-DX-A8BO        TCGA-DX-A8BP        TCGA-DX-A8BQ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BR        TCGA-DX-A8BS        TCGA-DX-A8BT        TCGA-DX-A8BU 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-A8BV        TCGA-DX-A8BX        TCGA-DX-AATS        TCGA-DX-AB2F 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2G        TCGA-DX-AB2H        TCGA-DX-AB2J        TCGA-DX-AB2O 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2P        TCGA-DX-AB2Q        TCGA-DX-AB2S        TCGA-DX-AB2T 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2V        TCGA-DX-AB2W        TCGA-DX-AB2X        TCGA-DX-AB2Z 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB30        TCGA-DX-AB32        TCGA-DX-AB35        TCGA-DX-AB36 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB37        TCGA-DX-AB3B        TCGA-DX-AB3C        TCGA-FX-A2QS 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A76Y        TCGA-FX-A8OO        TCGA-HB-A2OT        TCGA-HB-A3YV 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-HB-A43Z        TCGA-HB-A5W3        TCGA-HS-A5N7        TCGA-HS-A5N8 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IE-A4EH        TCGA-IE-A4EI        TCGA-IE-A4EJ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IF-A4AJ        TCGA-IF-A4AK        TCGA-IS-A3K7        TCGA-IS-A3KA 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IW-A3M4        TCGA-IW-A3M5        TCGA-IW-A3M6        TCGA-JV-A5VE 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-JV-A5VF        TCGA-JV-A75J        TCGA-K1-A3PO        TCGA-K1-A6RT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-K1-A6RU        TCGA-K1-A6RV        TCGA-KD-A5QS        TCGA-KD-A5QT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-KD-A5QU        TCGA-KF-A41W        TCGA-LI-A67I        TCGA-LI-A9QH 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MB-A5Y8        TCGA-MB-A5Y9        TCGA-MB-A5YA        TCGA-MB-A8JK 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MB-A8JL        TCGA-MJ-A68H        TCGA-MJ-A850        TCGA-MO-A47R 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-PC-A5DK        TCGA-PC-A5DN        TCGA-PC-A5DO        TCGA-PT-A8TR 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QC-A6FX        TCGA-QC-A7B5        TCGA-QC-AA9N        TCGA-QQ-A5VB 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QQ-A5VC        TCGA-QQ-A5VD        TCGA-QQ-A8VD        TCGA-QQ-A8VG 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QQ-A8VH        TCGA-RN-AAAQ        TCGA-SG-A6Z4        TCGA-SG-A6Z7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SG-A849        TCGA-SI-A71O        TCGA-SI-A71P        TCGA-SI-A71Q 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SI-AA8B        TCGA-SI-AA8C        TCGA-UE-A6QU        TCGA-VT-AB3D 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XO        TCGA-WK-A8XQ        TCGA-WK-A8XS        TCGA-WK-A8XT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XX        TCGA-WK-A8XY        TCGA-WK-A8XZ        TCGA-WK-A8Y0 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WP-A9GB        TCGA-X2-A95T        TCGA-X6-A7W8        TCGA-X6-A7WC 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X6-A8C2        TCGA-X6-A8C3        TCGA-X6-A8C5        TCGA-X6-A8C6 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X6-A8C7        TCGA-X9-A971        TCGA-X9-A973        TCGA-Z4-A8JB 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-Z4-A9VC        TCGA-Z4-AAPF        TCGA-Z4-AAPG 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 

Clustering(18) Variable = COL18A1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL18A1 MUTATED        2      2      3      0
  COL18A1 WILD-TYPE     60     81     67     25
D18V1, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               2                60
  CLUS_2               2                81
  CLUS_3               3                67
  CLUS_4               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  COL18A1 MUTATED        2      3      1      0      1      0      0
  COL18A1 WILD-TYPE     43     43     56     35     44     13      3
D18V2, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               2                43
  CLUS_2               3                43
  CLUS_3               1                56
  CLUS_4               0                35
  CLUS_5               1                44
  CLUS_6               0                13
  CLUS_7               0                 3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL18A1 MUTATED        1      1      1      4
  COL18A1 WILD-TYPE     54     41     53     52
D18V3, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               1                54
  CLUS_2               1                41
  CLUS_3               1                53
  CLUS_4               4                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  COL18A1 MUTATED        1      1      3      1      1      0
  COL18A1 WILD-TYPE     24     33     43     60     18     22
D18V4, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               1                24
  CLUS_2               1                33
  CLUS_3               3                43
  CLUS_4               1                60
  CLUS_5               1                18
  CLUS_6               0                22
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  COL18A1 MUTATED        3      1      2
  COL18A1 WILD-TYPE    106     70     60
D18V5, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               3               106
  CLUS_2               1                70
  CLUS_3               2                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  COL18A1 MUTATED        1      0      1      2      2      0      0
  COL18A1 WILD-TYPE     41     23     46     44     24     25     33
D18V6, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               1                41
  CLUS_2               0                23
  CLUS_3               1                46
  CLUS_4               2                44
  CLUS_5               2                24
  CLUS_6               0                25
  CLUS_7               0                33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  COL18A1 MUTATED        3      2      2
  COL18A1 WILD-TYPE     99     47     90
D18V7, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               3                99
  CLUS_2               2                47
  CLUS_3               2                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL18A1 MUTATED        2      3      2      0
  COL18A1 WILD-TYPE     74     47     93     22
D18V8, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               2                74
  CLUS_2               3                47
  CLUS_3               2                93
  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
  COL18A1 MUTATED        2      1      2
  COL18A1 WILD-TYPE     77     59     44
D18V9, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               2                77
  CLUS_2               1                59
  CLUS_3               2                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  COL18A1 MUTATED        2      0      1      0      0      0      2      0
  COL18A1 WILD-TYPE     22     29     32     24     11     21     19     22
D18V10, multiclass
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                29
  CLUS_3               1                32
  CLUS_4               0                24
  CLUS_5               0                11
  CLUS_6               0                21
  CLUS_7               2                19
  CLUS_8               0                22
[1] 8 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 = LHCGR MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LHCGR MUTATED        1      1      4      0
  LHCGR WILD-TYPE     61     82     66     25
D19V1, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1              61
  CLUS_2             1              82
  CLUS_3             4              66
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LHCGR MUTATED        1      0      0      2      3      0      0
  LHCGR WILD-TYPE     44     46     57     33     42     13      3
D19V2, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1              44
  CLUS_2             0              46
  CLUS_3             0              57
  CLUS_4             2              33
  CLUS_5             3              42
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LHCGR MUTATED        0      3      0      2
  LHCGR WILD-TYPE     55     39     54     54
D19V3, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             0              55
  CLUS_2             3              39
  CLUS_3             0              54
  CLUS_4             2              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  LHCGR MUTATED        0      0      3      0      1      1
  LHCGR WILD-TYPE     25     34     43     61     18     21
D19V4, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             0              25
  CLUS_2             0              34
  CLUS_3             3              43
  CLUS_4             0              61
  CLUS_5             1              18
  CLUS_6             1              21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LHCGR MUTATED        4      0      2
  LHCGR WILD-TYPE    105     71     60
D19V5, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             4             105
  CLUS_2             0              71
  CLUS_3             2              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LHCGR MUTATED        0      1      0      2      3      0      0
  LHCGR WILD-TYPE     42     22     47     44     23     25     33
D19V6, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              22
  CLUS_3             0              47
  CLUS_4             2              44
  CLUS_5             3              23
  CLUS_6             0              25
  CLUS_7             0              33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LHCGR MUTATED        3      0      3
  LHCGR WILD-TYPE     99     49     89
D19V7, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             3              99
  CLUS_2             0              49
  CLUS_3             3              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LHCGR MUTATED        1      1      2      2
  LHCGR WILD-TYPE     75     49     93     20
D19V8, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1              75
  CLUS_2             1              49
  CLUS_3             2              93
  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
  LHCGR MUTATED        2      1      2
  LHCGR WILD-TYPE     77     59     44
D19V9, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             2              77
  CLUS_2             1              59
  CLUS_3             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  LHCGR MUTATED        0      0      0      2      0      0      1      2
  LHCGR WILD-TYPE     24     29     33     22     11     21     20     20
D19V10, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             0              24
  CLUS_2             0              29
  CLUS_3             0              33
  CLUS_4             2              22
  CLUS_5             0              11
  CLUS_6             0              21
  CLUS_7             1              20
  CLUS_8             2              20
[1] 8 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 = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        1      3      5      1
  NF1 WILD-TYPE     61     80     65     24
D20V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            61
  CLUS_2           3            80
  CLUS_3           5            65
  CLUS_4           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NF1 MUTATED        1      5      0      2      2      0      0
  NF1 WILD-TYPE     44     41     57     33     43     13      3
D20V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            44
  CLUS_2           5            41
  CLUS_3           0            57
  CLUS_4           2            33
  CLUS_5           2            43
  CLUS_6           0            13
  CLUS_7           0             3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        3      2      0      4
  NF1 WILD-TYPE     52     40     54     52
D20V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            52
  CLUS_2           2            40
  CLUS_3           0            54
  CLUS_4           4            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NF1 MUTATED        1      1      3      0      0      4
  NF1 WILD-TYPE     24     33     43     61     19     18
D20V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            24
  CLUS_2           1            33
  CLUS_3           3            43
  CLUS_4           0            61
  CLUS_5           0            19
  CLUS_6           4            18
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        6      0      4
  NF1 WILD-TYPE    103     71     58
D20V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           6           103
  CLUS_2           0            71
  CLUS_3           4            58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NF1 MUTATED        1      0      0      4      4      0      1
  NF1 WILD-TYPE     41     23     47     42     22     25     32
D20V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            41
  CLUS_2           0            23
  CLUS_3           0            47
  CLUS_4           4            42
  CLUS_5           4            22
  CLUS_6           0            25
  CLUS_7           1            32
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        4      3      3
  NF1 WILD-TYPE     98     46     89
D20V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            98
  CLUS_2           3            46
  CLUS_3           3            89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        2      3      4      1
  NF1 WILD-TYPE     74     47     91     21
D20V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            74
  CLUS_2           3            47
  CLUS_3           4            91
  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
  NF1 MUTATED        1      2      5
  NF1 WILD-TYPE     78     58     41
D20V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            78
  CLUS_2           2            58
  CLUS_3           5            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  NF1 MUTATED        0      0      0      4      0      0      3      1
  NF1 WILD-TYPE     24     29     33     20     11     21     18     21
D20V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            24
  CLUS_2           0            29
  CLUS_3           0            33
  CLUS_4           4            20
  CLUS_5           0            11
  CLUS_6           0            21
  CLUS_7           3            18
  CLUS_8           1            21
[1] 8 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 = FOXD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXD2 MUTATED        0      2      1      0
  FOXD2 WILD-TYPE     62     81     69     25
D21V1, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             0              62
  CLUS_2             2              81
  CLUS_3             1              69
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FOXD2 MUTATED        0      0      1      1      1      0      0
  FOXD2 WILD-TYPE     45     46     56     34     44     13      3
D21V2, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             0              45
  CLUS_2             0              46
  CLUS_3             1              56
  CLUS_4             1              34
  CLUS_5             1              44
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXD2 MUTATED        0      0      1      1
  FOXD2 WILD-TYPE     55     42     53     55
D21V3, multiclass
[1] "Remove cluster labels:" "FOXD2 MUTATED"         
clus
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              2             205 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HV 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-3B-A9I1      TCGA-3R-A8YX      TCGA-DX-A1KU      TCGA-DX-A1KW 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1KX      TCGA-DX-A1KY      TCGA-DX-A1KZ      TCGA-DX-A1L0 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1L1      TCGA-DX-A1L2      TCGA-DX-A1L3      TCGA-DX-A1L4 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A23R      TCGA-DX-A23T      TCGA-DX-A23U      TCGA-DX-A23V 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A23Y      TCGA-DX-A240      TCGA-DX-A2IZ      TCGA-DX-A2J0 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A2J1      TCGA-DX-A2J4      TCGA-DX-A3LS      TCGA-DX-A3LT 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3LU      TCGA-DX-A3LW      TCGA-DX-A3LY      TCGA-DX-A3M1 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3M2      TCGA-DX-A3U5      TCGA-DX-A3U6      TCGA-DX-A3U7 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3U8      TCGA-DX-A3U9      TCGA-DX-A3UA      TCGA-DX-A3UB 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE      TCGA-DX-A3UF 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L      TCGA-DX-A48N 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R      TCGA-DX-A48U 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8      TCGA-DX-A6B9 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE      TCGA-DX-A6BF 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK      TCGA-DX-A6YQ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6YU      TCGA-DX-A6YZ      TCGA-DX-A6Z0      TCGA-DX-A6Z2 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7EF      TCGA-DX-A7EI      TCGA-DX-A7EL      TCGA-DX-A7EM 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7EN      TCGA-DX-A7EQ      TCGA-DX-A7ER      TCGA-DX-A7ES 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7ET      TCGA-DX-A7EU      TCGA-DX-A8BG      TCGA-DX-A8BH 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BJ      TCGA-DX-A8BK      TCGA-DX-A8BL      TCGA-DX-A8BM 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BN      TCGA-DX-A8BO      TCGA-DX-A8BP      TCGA-DX-A8BQ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BR      TCGA-DX-A8BS      TCGA-DX-A8BT      TCGA-DX-A8BU 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BV      TCGA-DX-A8BX      TCGA-DX-A8BZ      TCGA-DX-AATS 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2E      TCGA-DX-AB2F      TCGA-DX-AB2G      TCGA-DX-AB2H 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2J      TCGA-DX-AB2O      TCGA-DX-AB2P      TCGA-DX-AB2Q 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2S      TCGA-DX-AB2T      TCGA-DX-AB2V      TCGA-DX-AB2W 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2X      TCGA-DX-AB2Z      TCGA-DX-AB30      TCGA-DX-AB32 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB35      TCGA-DX-AB36      TCGA-DX-AB37      TCGA-DX-AB3A 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB3B      TCGA-DX-AB3C      TCGA-FX-A2QS      TCGA-FX-A3NJ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-FX-A3RE      TCGA-FX-A3TO      TCGA-HB-A3L4      TCGA-HB-A3YV 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-HB-A43Z      TCGA-HB-A5W3      TCGA-HS-A5N7      TCGA-HS-A5N8 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI      TCGA-IE-A4EJ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IE-A4EK      TCGA-IE-A6BZ      TCGA-IS-A3K6      TCGA-IS-A3K7 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IS-A3K8      TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IW-A3M6      TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-K1-A3PO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT      TCGA-K1-A6RU 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-K1-A6RV      TCGA-KF-A41W      TCGA-LI-A67I      TCGA-LI-A9QH 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA      TCGA-MB-A8JK 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-MB-A8JL      TCGA-MO-A47R      TCGA-N1-A6IA      TCGA-PC-A5DK 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO      TCGA-PT-A8TR 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N      TCGA-QQ-A5V2 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB      TCGA-QQ-A5VC 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A5VD      TCGA-QQ-A8VG      TCGA-QQ-A8VH      TCGA-RN-A68Q 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-RN-AAAQ      TCGA-SG-A6Z4      TCGA-SG-A6Z7      TCGA-SG-A849 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-SI-A71O      TCGA-SI-A71P      TCGA-SI-A71Q      TCGA-SI-AA8B 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-SI-AA8C      TCGA-UE-A6QT      TCGA-UE-A6QU      TCGA-VT-A80G 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X6-A7W8 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2      TCGA-X6-A8C3 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6      TCGA-X6-A8C7 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC      TCGA-Z4-AAPF 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-Z4-AAPG 
"FOXD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FOXD2 MUTATED        0      0      1      1      0      0
  FOXD2 WILD-TYPE     25     34     45     60     19     22
D21V4, multiclass
[1] "Remove cluster labels:" "FOXD2 MUTATED"         
clus
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              2             205 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HV 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-3B-A9I1      TCGA-3R-A8YX      TCGA-DX-A1KU      TCGA-DX-A1KW 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1KX      TCGA-DX-A1KY      TCGA-DX-A1KZ      TCGA-DX-A1L0 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1L1      TCGA-DX-A1L2      TCGA-DX-A1L3      TCGA-DX-A1L4 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A23R      TCGA-DX-A23T      TCGA-DX-A23U      TCGA-DX-A23V 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A23Y      TCGA-DX-A240      TCGA-DX-A2IZ      TCGA-DX-A2J0 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A2J1      TCGA-DX-A2J4      TCGA-DX-A3LS      TCGA-DX-A3LT 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3LU      TCGA-DX-A3LW      TCGA-DX-A3LY      TCGA-DX-A3M1 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3M2      TCGA-DX-A3U5      TCGA-DX-A3U6      TCGA-DX-A3U7 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3U8      TCGA-DX-A3U9      TCGA-DX-A3UA      TCGA-DX-A3UB 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE      TCGA-DX-A3UF 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L      TCGA-DX-A48N 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R      TCGA-DX-A48U 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8      TCGA-DX-A6B9 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE      TCGA-DX-A6BF 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK      TCGA-DX-A6YQ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6YU      TCGA-DX-A6YZ      TCGA-DX-A6Z0      TCGA-DX-A6Z2 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7EF      TCGA-DX-A7EI      TCGA-DX-A7EL      TCGA-DX-A7EM 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7EN      TCGA-DX-A7EQ      TCGA-DX-A7ER      TCGA-DX-A7ES 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7ET      TCGA-DX-A7EU      TCGA-DX-A8BG      TCGA-DX-A8BH 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BJ      TCGA-DX-A8BK      TCGA-DX-A8BL      TCGA-DX-A8BM 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BN      TCGA-DX-A8BO      TCGA-DX-A8BP      TCGA-DX-A8BQ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BR      TCGA-DX-A8BS      TCGA-DX-A8BT      TCGA-DX-A8BU 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BV      TCGA-DX-A8BX      TCGA-DX-A8BZ      TCGA-DX-AATS 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2E      TCGA-DX-AB2F      TCGA-DX-AB2G      TCGA-DX-AB2H 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2J      TCGA-DX-AB2O      TCGA-DX-AB2P      TCGA-DX-AB2Q 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2S      TCGA-DX-AB2T      TCGA-DX-AB2V      TCGA-DX-AB2W 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2X      TCGA-DX-AB2Z      TCGA-DX-AB30      TCGA-DX-AB32 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB35      TCGA-DX-AB36      TCGA-DX-AB37      TCGA-DX-AB3A 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB3B      TCGA-DX-AB3C      TCGA-FX-A2QS      TCGA-FX-A3NJ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-FX-A3RE      TCGA-FX-A3TO      TCGA-HB-A3L4      TCGA-HB-A3YV 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-HB-A43Z      TCGA-HB-A5W3      TCGA-HS-A5N7      TCGA-HS-A5N8 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI      TCGA-IE-A4EJ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IE-A4EK      TCGA-IE-A6BZ      TCGA-IS-A3K6      TCGA-IS-A3K7 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IS-A3K8      TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IW-A3M6      TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-K1-A3PO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT      TCGA-K1-A6RU 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-K1-A6RV      TCGA-KF-A41W      TCGA-LI-A67I      TCGA-LI-A9QH 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA      TCGA-MB-A8JK 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-MB-A8JL      TCGA-MO-A47R      TCGA-N1-A6IA      TCGA-PC-A5DK 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO      TCGA-PT-A8TR 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N      TCGA-QQ-A5V2 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB      TCGA-QQ-A5VC 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A5VD      TCGA-QQ-A8VG      TCGA-QQ-A8VH      TCGA-RN-A68Q 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-RN-AAAQ      TCGA-SG-A6Z4      TCGA-SG-A6Z7      TCGA-SG-A849 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-SI-A71O      TCGA-SI-A71P      TCGA-SI-A71Q      TCGA-SI-AA8B 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-SI-AA8C      TCGA-UE-A6QT      TCGA-UE-A6QU      TCGA-VT-A80G 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X6-A7W8 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2      TCGA-X6-A8C3 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6      TCGA-X6-A8C7 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC      TCGA-Z4-AAPF 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-Z4-AAPG 
"FOXD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXD2 MUTATED        1      1      1
  FOXD2 WILD-TYPE    108     70     61
D21V5, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             1             108
  CLUS_2             1              70
  CLUS_3             1              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FOXD2 MUTATED        0      0      0      1      1      1      0
  FOXD2 WILD-TYPE     42     23     47     45     25     24     33
D21V6, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             0              23
  CLUS_3             0              47
  CLUS_4             1              45
  CLUS_5             1              25
  CLUS_6             1              24
  CLUS_7             0              33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXD2 MUTATED        1      1      1
  FOXD2 WILD-TYPE    101     48     91
D21V7, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             1             101
  CLUS_2             1              48
  CLUS_3             1              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXD2 MUTATED        1      0      1      1
  FOXD2 WILD-TYPE     75     50     94     21
D21V8, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             1              75
  CLUS_2             0              50
  CLUS_3             1              94
  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
  FOXD2 MUTATED        1      1      1
  FOXD2 WILD-TYPE     78     59     45
D21V9, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             1              78
  CLUS_2             1              59
  CLUS_3             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  FOXD2 MUTATED        0      0      0      0      1      0      1      1
  FOXD2 WILD-TYPE     24     29     33     24     10     21     20     21
D21V10, multiclass
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  CLUS_1             0              24
  CLUS_2             0              29
  CLUS_3             0              33
  CLUS_4             0              24
  CLUS_5             1              10
  CLUS_6             0              21
  CLUS_7             1              20
  CLUS_8             1              21
[1] 8 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 = MMP17 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP17 MUTATED        0      2      1      0
  MMP17 WILD-TYPE     62     81     69     25
D22V1, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             0              62
  CLUS_2             2              81
  CLUS_3             1              69
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MMP17 MUTATED        1      0      0      2      0      0      0
  MMP17 WILD-TYPE     44     46     57     33     45     13      3
D22V2, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             1              44
  CLUS_2             0              46
  CLUS_3             0              57
  CLUS_4             2              33
  CLUS_5             0              45
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP17 MUTATED        2      1      0      0
  MMP17 WILD-TYPE     53     41     54     56
D22V3, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             2              53
  CLUS_2             1              41
  CLUS_3             0              54
  CLUS_4             0              56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  MMP17 MUTATED        0      0      1      1      0      1
  MMP17 WILD-TYPE     25     34     45     60     19     21
D22V4, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             0              25
  CLUS_2             0              34
  CLUS_3             1              45
  CLUS_4             1              60
  CLUS_5             0              19
  CLUS_6             1              21
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP17 MUTATED        1      0      2
  MMP17 WILD-TYPE    108     71     60
D22V5, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             1             108
  CLUS_2             0              71
  CLUS_3             2              60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MMP17 MUTATED        1      0      0      1      1      0      0
  MMP17 WILD-TYPE     41     23     47     45     25     25     33
D22V6, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             1              41
  CLUS_2             0              23
  CLUS_3             0              47
  CLUS_4             1              45
  CLUS_5             1              25
  CLUS_6             0              25
  CLUS_7             0              33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP17 MUTATED        3      0      0
  MMP17 WILD-TYPE     99     49     92
D22V7, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             3              99
  CLUS_2             0              49
  CLUS_3             0              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP17 MUTATED        1      1      0      1
  MMP17 WILD-TYPE     75     49     95     21
D22V8, multiclass
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  CLUS_1             1              75
  CLUS_2             1              49
  CLUS_3             0              95
  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
  MMP17 MUTATED        2      0      0
  MMP17 WILD-TYPE     77     60     46
D22V9, multiclass
[1] "Remove cluster labels:" "MMP17 MUTATED"         
clus
  MMP17 MUTATED MMP17 WILD-TYPE 
              2             183 
     TCGA-3B-A9HI      TCGA-3B-A9HL      TCGA-3B-A9HP      TCGA-3B-A9HQ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-3B-A9HR      TCGA-3B-A9HS      TCGA-3B-A9HU      TCGA-3B-A9HX 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-3B-A9HY      TCGA-3B-A9HZ      TCGA-3B-A9I1      TCGA-3B-A9I3 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-3R-A8YX      TCGA-DX-A1KU      TCGA-DX-A1KW      TCGA-DX-A1KX 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A1KY      TCGA-DX-A1KZ      TCGA-DX-A1L0      TCGA-DX-A23R 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A23T      TCGA-DX-A23V      TCGA-DX-A240      TCGA-DX-A2IZ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A3LS      TCGA-DX-A3LW 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A3LY      TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A3U6      TCGA-DX-A3U7      TCGA-DX-A3U8      TCGA-DX-A3U9 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A3UA      TCGA-DX-A48K      TCGA-DX-A48L      TCGA-DX-A48N 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A48O      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6YQ      TCGA-DX-A6YR      TCGA-DX-A6YU 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A6YX      TCGA-DX-A6YZ      TCGA-DX-A7EI      TCGA-DX-A7EQ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU      TCGA-DX-A8BG 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK      TCGA-DX-A8BL 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO      TCGA-DX-A8BP 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS      TCGA-DX-A8BT 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-AATS      TCGA-DX-AB2F 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB2G      TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3NK      TCGA-FX-A3RE 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-FX-A3TO      TCGA-FX-A76Y      TCGA-FX-A8OO      TCGA-HB-A2OT 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-HB-A3YV      TCGA-HB-A43Z      TCGA-HB-A5W3      TCGA-HS-A5N7 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-HS-A5N8      TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-IE-A4EJ      TCGA-IF-A4AJ      TCGA-IF-A4AK      TCGA-IS-A3K7 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-JV-A75J      TCGA-K1-A3PO 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-K1-A6RT      TCGA-K1-A6RU      TCGA-K1-A6RV      TCGA-KD-A5QS 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-KD-A5QT      TCGA-KD-A5QU      TCGA-KF-A41W      TCGA-LI-A67I 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MJ-A68H      TCGA-MJ-A850 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-MO-A47R      TCGA-PC-A5DK      TCGA-PC-A5DN      TCGA-PC-A5DO 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-QQ-A5VB      TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VD 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-QQ-A8VG      TCGA-QQ-A8VH      TCGA-RN-AAAQ      TCGA-SG-A6Z4 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-SG-A6Z7      TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-SI-A71Q      TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QU 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-VT-AB3D      TCGA-WK-A8XO      TCGA-WK-A8XQ      TCGA-WK-A8XS 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-WK-A8XT      TCGA-WK-A8XX      TCGA-WK-A8XY      TCGA-WK-A8XZ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X2-A95T      TCGA-X6-A7W8 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-X6-A7WC      TCGA-X6-A8C2      TCGA-X6-A8C3      TCGA-X6-A8C5 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-X6-A8C6      TCGA-X6-A8C7      TCGA-X9-A971      TCGA-X9-A973 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-Z4-A8JB      TCGA-Z4-A9VC      TCGA-Z4-AAPG 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  MMP17 MUTATED        0      1      0      0      0      0      0      1
  MMP17 WILD-TYPE     24     28     33     24     11     21     21     21
D22V10, multiclass
[1] "Remove cluster labels:" "MMP17 MUTATED"         
clus
  MMP17 MUTATED MMP17 WILD-TYPE 
              2             183 
     TCGA-3B-A9HI      TCGA-3B-A9HL      TCGA-3B-A9HP      TCGA-3B-A9HQ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-3B-A9HR      TCGA-3B-A9HS      TCGA-3B-A9HU      TCGA-3B-A9HX 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-3B-A9HY      TCGA-3B-A9HZ      TCGA-3B-A9I1      TCGA-3B-A9I3 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-3R-A8YX      TCGA-DX-A1KU      TCGA-DX-A1KW      TCGA-DX-A1KX 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A1KY      TCGA-DX-A1KZ      TCGA-DX-A1L0      TCGA-DX-A23R 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A23T      TCGA-DX-A23V      TCGA-DX-A240      TCGA-DX-A2IZ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A3LS      TCGA-DX-A3LW 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A3LY      TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A3U6      TCGA-DX-A3U7      TCGA-DX-A3U8      TCGA-DX-A3U9 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A3UA      TCGA-DX-A48K      TCGA-DX-A48L      TCGA-DX-A48N 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A48O      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6YQ      TCGA-DX-A6YR      TCGA-DX-A6YU 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A6YX      TCGA-DX-A6YZ      TCGA-DX-A7EI      TCGA-DX-A7EQ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU      TCGA-DX-A8BG 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK      TCGA-DX-A8BL 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO      TCGA-DX-A8BP 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS      TCGA-DX-A8BT 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-AATS      TCGA-DX-AB2F 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB2G      TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3NK      TCGA-FX-A3RE 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-FX-A3TO      TCGA-FX-A76Y      TCGA-FX-A8OO      TCGA-HB-A2OT 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-HB-A3YV      TCGA-HB-A43Z      TCGA-HB-A5W3      TCGA-HS-A5N7 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-HS-A5N8      TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-IE-A4EJ      TCGA-IF-A4AJ      TCGA-IF-A4AK      TCGA-IS-A3K7 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-JV-A75J      TCGA-K1-A3PO 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-K1-A6RT      TCGA-K1-A6RU      TCGA-K1-A6RV      TCGA-KD-A5QS 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-KD-A5QT      TCGA-KD-A5QU      TCGA-KF-A41W      TCGA-LI-A67I 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MJ-A68H      TCGA-MJ-A850 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-MO-A47R      TCGA-PC-A5DK      TCGA-PC-A5DN      TCGA-PC-A5DO 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-QQ-A5VB      TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VD 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-QQ-A8VG      TCGA-QQ-A8VH      TCGA-RN-AAAQ      TCGA-SG-A6Z4 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-SG-A6Z7      TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-SI-A71Q      TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QU 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-VT-AB3D      TCGA-WK-A8XO      TCGA-WK-A8XQ      TCGA-WK-A8XS 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-WK-A8XT      TCGA-WK-A8XX      TCGA-WK-A8XY      TCGA-WK-A8XZ 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X2-A95T      TCGA-X6-A7W8 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-X6-A7WC      TCGA-X6-A8C2      TCGA-X6-A8C3      TCGA-X6-A8C5 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-X6-A8C6      TCGA-X6-A8C7      TCGA-X9-A971      TCGA-X9-A973 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 
     TCGA-Z4-A8JB      TCGA-Z4-A9VC      TCGA-Z4-AAPG 
"MMP17 WILD-TYPE" "MMP17 WILD-TYPE" "MMP17 WILD-TYPE" 

Clustering(23) Variable = ASTE1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASTE1 MUTATED        0      0      3      0
  ASTE1 WILD-TYPE     62     83     67     25
D23V1, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             0              62
  CLUS_2             0              83
  CLUS_3             3              67
  CLUS_4             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ASTE1 MUTATED        3      0      0      0      0      0      0
  ASTE1 WILD-TYPE     42     46     57     35     45     13      3
D23V2, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             3              42
  CLUS_2             0              46
  CLUS_3             0              57
  CLUS_4             0              35
  CLUS_5             0              45
  CLUS_6             0              13
  CLUS_7             0               3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASTE1 MUTATED        1      1      0      0
  ASTE1 WILD-TYPE     54     41     54     56
D23V3, multiclass
[1] "Remove cluster labels:" "ASTE1 MUTATED"         
clus
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              2             205 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HV 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-3B-A9I1      TCGA-3B-A9I3      TCGA-3R-A8YX      TCGA-DX-A1KU 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A1KW      TCGA-DX-A1KX      TCGA-DX-A1KY      TCGA-DX-A1KZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A1L0      TCGA-DX-A1L1      TCGA-DX-A1L2      TCGA-DX-A1L3 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A1L4      TCGA-DX-A23R      TCGA-DX-A23T      TCGA-DX-A23U 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A23V      TCGA-DX-A23Y      TCGA-DX-A240      TCGA-DX-A2IZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A2J4      TCGA-DX-A3LS 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3LT      TCGA-DX-A3LU      TCGA-DX-A3LW      TCGA-DX-A3LY 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5      TCGA-DX-A3U6 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3U7      TCGA-DX-A3U8      TCGA-DX-A3U9      TCGA-DX-A3UA 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3UB      TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3UF      TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A48N      TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A48U      TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6B9      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6YQ      TCGA-DX-A6YU      TCGA-DX-A6YX      TCGA-DX-A6YZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6Z0      TCGA-DX-A6Z2      TCGA-DX-A7EF      TCGA-DX-A7EI 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A7EL      TCGA-DX-A7EM      TCGA-DX-A7EN      TCGA-DX-A7EQ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A7ER      TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BG      TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BL      TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BP      TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BT      TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-A8BZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AATS      TCGA-DX-AB2E      TCGA-DX-AB2F      TCGA-DX-AB2G 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O      TCGA-DX-AB2P 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T      TCGA-DX-AB2V 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z      TCGA-DX-AB30 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36      TCGA-DX-AB37 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C      TCGA-FX-A2QS 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-FX-A3NJ      TCGA-FX-A3RE      TCGA-FX-A3TO      TCGA-HB-A3L4 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-HB-A3YV      TCGA-HB-A43Z      TCGA-HB-A5W3      TCGA-HS-A5N7 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-HS-A5N8      TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-IE-A4EJ      TCGA-IE-A4EK      TCGA-IE-A6BZ      TCGA-IS-A3K6 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-IS-A3K7      TCGA-IS-A3K8      TCGA-IS-A3KA      TCGA-IW-A3M4 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-IW-A3M5      TCGA-IW-A3M6      TCGA-JV-A5VE      TCGA-JV-A5VF 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-K1-A3PO      TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-K1-A6RU      TCGA-K1-A6RV      TCGA-KF-A41W      TCGA-LI-A67I 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MO-A47R      TCGA-N1-A6IA 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-PC-A5DK      TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-QQ-A5V2      TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VG      TCGA-QQ-A8VH 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-RN-A68Q      TCGA-RN-AAAQ      TCGA-SG-A6Z4      TCGA-SG-A6Z7 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P      TCGA-SI-A71Q 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QT      TCGA-UE-A6QU 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-VT-A80G      TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-X6-A7W8      TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-X6-A8C3      TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C7 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC      TCGA-Z4-AAPF 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-Z4-AAPG 
"ASTE1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ASTE1 MUTATED        0      0      2      0      0      0
  ASTE1 WILD-TYPE     25     34     44     61     19     22
D23V4, multiclass
[1] "Remove cluster labels:" "ASTE1 MUTATED"         
clus
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              2             205 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HV 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-3B-A9I1      TCGA-3B-A9I3      TCGA-3R-A8YX      TCGA-DX-A1KU 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A1KW      TCGA-DX-A1KX      TCGA-DX-A1KY      TCGA-DX-A1KZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A1L0      TCGA-DX-A1L1      TCGA-DX-A1L2      TCGA-DX-A1L3 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A1L4      TCGA-DX-A23R      TCGA-DX-A23T      TCGA-DX-A23U 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A23V      TCGA-DX-A23Y      TCGA-DX-A240      TCGA-DX-A2IZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A2J4      TCGA-DX-A3LS 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3LT      TCGA-DX-A3LU      TCGA-DX-A3LW      TCGA-DX-A3LY 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5      TCGA-DX-A3U6 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3U7      TCGA-DX-A3U8      TCGA-DX-A3U9      TCGA-DX-A3UA 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3UB      TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A3UF      TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A48N      TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A48U      TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6B9      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6YQ      TCGA-DX-A6YU      TCGA-DX-A6YX      TCGA-DX-A6YZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A6Z0      TCGA-DX-A6Z2      TCGA-DX-A7EF      TCGA-DX-A7EI 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A7EL      TCGA-DX-A7EM      TCGA-DX-A7EN      TCGA-DX-A7EQ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A7ER      TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BG      TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BL      TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BP      TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-A8BT      TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-A8BZ 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AATS      TCGA-DX-AB2E      TCGA-DX-AB2F      TCGA-DX-AB2G 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O      TCGA-DX-AB2P 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T      TCGA-DX-AB2V 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z      TCGA-DX-AB30 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36      TCGA-DX-AB37 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C      TCGA-FX-A2QS 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-FX-A3NJ      TCGA-FX-A3RE      TCGA-FX-A3TO      TCGA-HB-A3L4 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-HB-A3YV      TCGA-HB-A43Z      TCGA-HB-A5W3      TCGA-HS-A5N7 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-HS-A5N8      TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-IE-A4EJ      TCGA-IE-A4EK      TCGA-IE-A6BZ      TCGA-IS-A3K6 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-IS-A3K7      TCGA-IS-A3K8      TCGA-IS-A3KA      TCGA-IW-A3M4 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-IW-A3M5      TCGA-IW-A3M6      TCGA-JV-A5VE      TCGA-JV-A5VF 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-K1-A3PO      TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-K1-A6RU      TCGA-K1-A6RV      TCGA-KF-A41W      TCGA-LI-A67I 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MO-A47R      TCGA-N1-A6IA 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-PC-A5DK      TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-QQ-A5V2      TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VG      TCGA-QQ-A8VH 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-RN-A68Q      TCGA-RN-AAAQ      TCGA-SG-A6Z4      TCGA-SG-A6Z7 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P      TCGA-SI-A71Q 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QT      TCGA-UE-A6QU 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-VT-A80G      TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-X6-A7W8      TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-X6-A8C3      TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C7 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC      TCGA-Z4-AAPF 
"ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" "ASTE1 WILD-TYPE" 
     TCGA-Z4-AAPG 
"ASTE1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASTE1 MUTATED        3      0      0
  ASTE1 WILD-TYPE    106     71     62
D23V5, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             3             106
  CLUS_2             0              71
  CLUS_3             0              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ASTE1 MUTATED        3      0      0      0      0      0      0
  ASTE1 WILD-TYPE     39     23     47     46     26     25     33
D23V6, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             3              39
  CLUS_2             0              23
  CLUS_3             0              47
  CLUS_4             0              46
  CLUS_5             0              26
  CLUS_6             0              25
  CLUS_7             0              33
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ASTE1 MUTATED        3      0      0
  ASTE1 WILD-TYPE     99     49     92
D23V7, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             3              99
  CLUS_2             0              49
  CLUS_3             0              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ASTE1 MUTATED        3      0      0      0
  ASTE1 WILD-TYPE     73     50     95     22
D23V8, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             3              73
  CLUS_2             0              50
  CLUS_3             0              95
  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
  ASTE1 MUTATED        3      0      0
  ASTE1 WILD-TYPE     76     60     46
D23V9, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             3              76
  CLUS_2             0              60
  CLUS_3             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
  ASTE1 MUTATED        0      2      0      0      0      1      0      0
  ASTE1 WILD-TYPE     24     27     33     24     11     20     21     22
D23V10, multiclass
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  CLUS_1             0              24
  CLUS_2             2              27
  CLUS_3             0              33
  CLUS_4             0              24
  CLUS_5             0              11
  CLUS_6             1              20
  CLUS_7             0              21
  CLUS_8             0              22
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
