[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/22542442/SARC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/22573933/transformed.cor.cli.txt"

nPatients in clinical file=261, in cluster file=247, common to both=247
[1]  17 247
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            85            162 
  TP53 MUTATED TP53 WILD-TYPE 
            85            162 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           24           223 
  RB1 MUTATED RB1 WILD-TYPE 
           24           223 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            36            211 
  ATRX MUTATED ATRX WILD-TYPE 
            36            211 
[1] "NUMBL MUTATION ANALYSIS"
[1] 3
  NUMBL MUTATED NUMBL WILD-TYPE 
              8             239 
  NUMBL MUTATED NUMBL WILD-TYPE 
              8             239 
[1] "MSH3 MUTATION ANALYSIS"
[1] 3
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            240 
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            240 
[1] "LTBP3 MUTATION ANALYSIS"
[1] 3
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             242 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             242 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              5             242 
  EOMES MUTATED EOMES WILD-TYPE 
              5             242 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            240 
  PTEN MUTATED PTEN WILD-TYPE 
             7            240 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                240 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                240 
[1] "CABLES1 MUTATION ANALYSIS"
[1] 3
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               244 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               244 
[1] "TRAF7 MUTATION ANALYSIS"
[1] 3
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             243 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             243 
[1] "LOR MUTATION ANALYSIS"
[1] 3
  LOR MUTATED LOR WILD-TYPE 
            6           241 
  LOR MUTATED LOR WILD-TYPE 
            6           241 
[1] "R3HDM1 MUTATION ANALYSIS"
[1] 3
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               4              243 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               4              243 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
            9           238 
  NF1 MUTATED NF1 WILD-TYPE 
            9           238 
[1] "COL4A3 MUTATION ANALYSIS"
[1] 3
  COL4A3 MUTATED COL4A3 WILD-TYPE 
               4              243 
  COL4A3 MUTATED COL4A3 WILD-TYPE 
               4              243 
[1] "MEGF9 MUTATION ANALYSIS"
[1] 3
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             244 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             244 
[1] "SCAP MUTATION ANALYSIS"
[1] 3
  SCAP MUTATED SCAP WILD-TYPE 
             3            244 
  SCAP MUTATED SCAP WILD-TYPE 
             3            244 
[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 247 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=5,	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 247 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=4, 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=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       31      8     16     28
  TP53 WILD-TYPE     59     50     22     29
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           31             59
  CLUS_2            8             50
  CLUS_3           16             22
  CLUS_4           28             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       13      6     38     28
  TP53 WILD-TYPE     42     46     30     44
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           13             42
  CLUS_2            6             46
  CLUS_3           38             30
  CLUS_4           28             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       10     15     27     21
  TP53 WILD-TYPE     46     27     28     36
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10             46
  CLUS_2           15             27
  CLUS_3           27             28
  CLUS_4           21             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        3     11     18     29      5      7
  TP53 WILD-TYPE     20     23     29     33     17     15
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             20
  CLUS_2           11             23
  CLUS_3           18             29
  CLUS_4           29             33
  CLUS_5            5             17
  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       35     37     12
  TP53 WILD-TYPE     75     35     51
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           35             75
  CLUS_2           37             35
  CLUS_3           12             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      7     26      4     12     11     12
  TP53 WILD-TYPE     31     14     22     42     17     14     21
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             31
  CLUS_2            7             14
  CLUS_3           26             22
  CLUS_4            4             42
  CLUS_5           12             17
  CLUS_6           11             14
  CLUS_7           12             21
[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       27     13     45
  TP53 WILD-TYPE     73     37     51
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           27             73
  CLUS_2           13             37
  CLUS_3           45             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
  TP53 MUTATED       25      5     53      2
  TP53 WILD-TYPE     54     31     57     19
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           25             54
  CLUS_2            5             31
  CLUS_3           53             57
  CLUS_4            2             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       11      3     24     10     16
  TP53 WILD-TYPE     45     23     20     13     23
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11             45
  CLUS_2            3             23
  CLUS_3           24             20
  CLUS_4           10             13
  CLUS_5           16             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED       15     25      9     11      4
  TP53 WILD-TYPE     40     21     12     31     20
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           15             40
  CLUS_2           25             21
  CLUS_3            9             12
  CLUS_4           11             31
  CLUS_5            4             20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        5      1      3     14
  RB1 WILD-TYPE     85     57     35     43
D2V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           5            85
  CLUS_2           1            57
  CLUS_3           3            35
  CLUS_4          14            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      3     15      3
  RB1 WILD-TYPE     52     49     53     69
D2V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            52
  CLUS_2           3            49
  CLUS_3          15            53
  CLUS_4           3            69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        3      1      9      6
  RB1 WILD-TYPE     53     41     46     51
D2V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            53
  CLUS_2           1            41
  CLUS_3           9            46
  CLUS_4           6            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               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     21     31     45     52     21     21
D2V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            21
  CLUS_2           3            31
  CLUS_3           2            45
  CLUS_4          10            52
  CLUS_5           1            21
  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    102     57     62
D2V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           8           102
  CLUS_2          15            57
  CLUS_3           1            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
  RB1 MUTATED        3      2     12      2      0      3      2
  RB1 WILD-TYPE     40     19     36     44     29     22     31
D2V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            40
  CLUS_2           2            19
  CLUS_3          12            36
  CLUS_4           2            44
  CLUS_5           0            29
  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    100     44     78
D2V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0           100
  CLUS_2           6            44
  CLUS_3          18            78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        1      2     21      0
  RB1 WILD-TYPE     78     34     89     21
D2V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            78
  CLUS_2           2            34
  CLUS_3          21            89
  CLUS_4           0            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 CLUS_4 CLUS_5
  RB1 MUTATED        0      3      8      2      5
  RB1 WILD-TYPE     56     23     36     21     34
D2V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            56
  CLUS_2           3            23
  CLUS_3           8            36
  CLUS_4           2            21
  CLUS_5           5            34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  RB1 MUTATED        0      9      6      3      0
  RB1 WILD-TYPE     55     37     15     39     24
D2V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           0            55
  CLUS_2           9            37
  CLUS_3           6            15
  CLUS_4           3            39
  CLUS_5           0            24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = ATRX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED       20      2      0     13
  ATRX WILD-TYPE     70     56     38     44
D3V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           20             70
  CLUS_2            2             56
  CLUS_3            0             38
  CLUS_4           13             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED        7      7      7     15
  ATRX WILD-TYPE     48     45     61     57
D3V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            7             48
  CLUS_2            7             45
  CLUS_3            7             61
  CLUS_4           15             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      4      6
  ATRX WILD-TYPE     47     31     51     51
D3V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            9             47
  CLUS_2           11             31
  CLUS_3            4             51
  CLUS_4            6             51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ATRX MUTATED        5      5      8      7      4      1
  ATRX WILD-TYPE     18     29     39     55     18     21
D3V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            5             18
  CLUS_2            5             29
  CLUS_3            8             39
  CLUS_4            7             55
  CLUS_5            4             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
  ATRX MUTATED       20      8      8
  ATRX WILD-TYPE     90     64     55
D3V5, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           20             90
  CLUS_2            8             64
  CLUS_3            8             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      2      5      5      6      6
  ATRX WILD-TYPE     33     19     46     41     24     19     27
D3V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           10             33
  CLUS_2            2             19
  CLUS_3            2             46
  CLUS_4            5             41
  CLUS_5            5             24
  CLUS_6            6             19
  CLUS_7            6             27
[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       16     10     10
  ATRX WILD-TYPE     84     40     86
D3V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           16             84
  CLUS_2           10             40
  CLUS_3           10             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED       15      5     15      1
  ATRX WILD-TYPE     64     31     95     20
D3V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           15             64
  CLUS_2            5             31
  CLUS_3           15             95
  CLUS_4            1             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 CLUS_4 CLUS_5
  ATRX MUTATED       10      5      3      4      7
  ATRX WILD-TYPE     46     21     41     19     32
D3V9, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           10             46
  CLUS_2            5             21
  CLUS_3            3             41
  CLUS_4            4             19
  CLUS_5            7             32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  ATRX MUTATED       14      4      5      6      0
  ATRX WILD-TYPE     41     42     16     36     24
D3V10, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           14             41
  CLUS_2            4             42
  CLUS_3            5             16
  CLUS_4            6             36
  CLUS_5            0             24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = NUMBL MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUMBL MUTATED        4      2      1      1
  NUMBL WILD-TYPE     86     56     37     56
D4V1, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             4              86
  CLUS_2             2              56
  CLUS_3             1              37
  CLUS_4             1              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
  NUMBL MUTATED        2      2      0      4
  NUMBL WILD-TYPE     53     50     68     68
D4V2, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             2              53
  CLUS_2             2              50
  CLUS_3             0              68
  CLUS_4             4              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUMBL MUTATED        2      2      1      2
  NUMBL WILD-TYPE     54     40     54     55
D4V3, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             2              54
  CLUS_2             2              40
  CLUS_3             1              54
  CLUS_4             2              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
  NUMBL MUTATED        0      0      5      1      1      0
  NUMBL WILD-TYPE     23     34     42     61     21     22
D4V4, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             0              23
  CLUS_2             0              34
  CLUS_3             5              42
  CLUS_4             1              61
  CLUS_5             1              21
  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      1      3
  NUMBL WILD-TYPE    106     71     60
D4V5, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             4             106
  CLUS_2             1              71
  CLUS_3             3              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
  NUMBL MUTATED        1      0      0      2      3      1      1
  NUMBL WILD-TYPE     42     21     48     44     26     24     32
D4V6, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             1              42
  CLUS_2             0              21
  CLUS_3             0              48
  CLUS_4             2              44
  CLUS_5             3              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
  NUMBL MUTATED        5      1      2
  NUMBL WILD-TYPE     95     49     94
D4V7, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             5              95
  CLUS_2             1              49
  CLUS_3             2              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NUMBL MUTATED        3      0      3      2
  NUMBL WILD-TYPE     76     36    107     19
D4V8, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             3              76
  CLUS_2             0              36
  CLUS_3             3             107
  CLUS_4             2              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NUMBL MUTATED        4      0      0      1      2
  NUMBL WILD-TYPE     52     26     44     22     37
D4V9, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             4              52
  CLUS_2             0              26
  CLUS_3             0              44
  CLUS_4             1              22
  CLUS_5             2              37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NUMBL MUTATED        5      0      1      1      0
  NUMBL WILD-TYPE     50     46     20     41     24
D4V10, multiclass
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  CLUS_1             5              50
  CLUS_2             0              46
  CLUS_3             1              20
  CLUS_4             1              41
  CLUS_5             0              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MSH3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MSH3 MUTATED        2      3      1      1
  MSH3 WILD-TYPE     88     55     37     56
D5V1, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             88
  CLUS_2            3             55
  CLUS_3            1             37
  CLUS_4            1             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
  MSH3 MUTATED        3      1      1      2
  MSH3 WILD-TYPE     52     51     67     70
D5V2, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            3             52
  CLUS_2            1             51
  CLUS_3            1             67
  CLUS_4            2             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MSH3 MUTATED        2      1      1      2
  MSH3 WILD-TYPE     54     41     54     55
D5V3, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             54
  CLUS_2            1             41
  CLUS_3            1             54
  CLUS_4            2             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
  MSH3 MUTATED        1      1      1      1      1      1
  MSH3 WILD-TYPE     22     33     46     61     21     21
D5V4, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            1             22
  CLUS_2            1             33
  CLUS_3            1             46
  CLUS_4            1             61
  CLUS_5            1             21
  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    106     70     62
D5V5, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            4            106
  CLUS_2            2             70
  CLUS_3            1             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
  MSH3 MUTATED        0      3      1      1      1      1      0
  MSH3 WILD-TYPE     43     18     47     45     28     24     33
D5V6, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            0             43
  CLUS_2            3             18
  CLUS_3            1             47
  CLUS_4            1             45
  CLUS_5            1             28
  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     98     48     94
D5V7, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             98
  CLUS_2            2             48
  CLUS_3            2             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MSH3 MUTATED        2      2      2      0
  MSH3 WILD-TYPE     77     34    108     21
D5V8, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             77
  CLUS_2            2             34
  CLUS_3            2            108
  CLUS_4            0             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 CLUS_4 CLUS_5
  MSH3 MUTATED        2      0      0      0      2
  MSH3 WILD-TYPE     54     26     44     23     37
D5V9, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            2             54
  CLUS_2            0             26
  CLUS_3            0             44
  CLUS_4            0             23
  CLUS_5            2             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MSH3 MUTATED        1      0      0      3      0
  MSH3 WILD-TYPE     54     46     21     39     24
D5V10, multiclass
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  CLUS_1            1             54
  CLUS_2            0             46
  CLUS_3            0             21
  CLUS_4            3             39
  CLUS_5            0             24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = LTBP3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LTBP3 MUTATED        3      0      2      0
  LTBP3 WILD-TYPE     87     58     36     57
D6V1, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             0              58
  CLUS_3             2              36
  CLUS_4             0              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        1      0      3      1
  LTBP3 WILD-TYPE     54     52     65     71
D6V2, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             1              54
  CLUS_2             0              52
  CLUS_3             3              65
  CLUS_4             1              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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     56     41     55     55
D6V3, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             1              41
  CLUS_3             0              55
  CLUS_4             2              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
  LTBP3 MUTATED        0      0      2      1      0      0
  LTBP3 WILD-TYPE     23     34     45     61     22     22
D6V4, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              23
  CLUS_2             0              34
  CLUS_3             2              45
  CLUS_4             1              61
  CLUS_5             0              22
  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    108     69     63
D6V5, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             2             108
  CLUS_2             3              69
  CLUS_3             0              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LTBP3 MUTATED        0      0      2      0      2      1      0
  LTBP3 WILD-TYPE     43     21     46     46     27     24     33
D6V6, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              43
  CLUS_2             0              21
  CLUS_3             2              46
  CLUS_4             0              46
  CLUS_5             2              27
  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    100     49     92
D6V7, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0             100
  CLUS_2             1              49
  CLUS_3             4              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
  LTBP3 MUTATED        0      0      5      0
  LTBP3 WILD-TYPE     79     36    105     21
D6V8, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              79
  CLUS_2             0              36
  CLUS_3             5             105
  CLUS_4             0              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 CLUS_4 CLUS_5
  LTBP3 MUTATED        0      0      3      0      1
  LTBP3 WILD-TYPE     56     26     41     23     38
D6V9, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             0              26
  CLUS_3             3              41
  CLUS_4             0              23
  CLUS_5             1              38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LTBP3 MUTATED        0      3      1      0      0
  LTBP3 WILD-TYPE     55     43     20     42     24
D6V10, multiclass
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  CLUS_1             0              55
  CLUS_2             3              43
  CLUS_3             1              20
  CLUS_4             0              42
  CLUS_5             0              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = EOMES MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EOMES MUTATED        3      1      0      1
  EOMES WILD-TYPE     87     57     38     56
D7V1, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3              87
  CLUS_2             1              57
  CLUS_3             0              38
  CLUS_4             1              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
  EOMES MUTATED        1      1      1      2
  EOMES WILD-TYPE     54     51     67     70
D7V2, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              54
  CLUS_2             1              51
  CLUS_3             1              67
  CLUS_4             2              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EOMES MUTATED        1      1      0      1
  EOMES WILD-TYPE     55     41     55     56
D7V3, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              55
  CLUS_2             1              41
  CLUS_3             0              55
  CLUS_4             1              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
  EOMES MUTATED        1      0      2      0      0      0
  EOMES WILD-TYPE     22     34     45     62     22     22
D7V4, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              22
  CLUS_2             0              34
  CLUS_3             2              45
  CLUS_4             0              62
  CLUS_5             0              22
  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      1      1
  EOMES WILD-TYPE    107     71     62
D7V5, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3             107
  CLUS_2             1              71
  CLUS_3             1              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
  EOMES MUTATED        1      0      1      1      1      0      1
  EOMES WILD-TYPE     42     21     47     45     28     25     32
D7V6, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             1              42
  CLUS_2             0              21
  CLUS_3             1              47
  CLUS_4             1              45
  CLUS_5             1              28
  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
  EOMES MUTATED        4      0      1
  EOMES WILD-TYPE     96     50     95
D7V7, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             4              96
  CLUS_2             0              50
  CLUS_3             1              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EOMES MUTATED        3      0      1      1
  EOMES WILD-TYPE     76     36    109     20
D7V8, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             3              76
  CLUS_2             0              36
  CLUS_3             1             109
  CLUS_4             1              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 CLUS_4 CLUS_5
  EOMES MUTATED        2      0      1      0      2
  EOMES WILD-TYPE     54     26     43     23     37
D7V9, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             2              54
  CLUS_2             0              26
  CLUS_3             1              43
  CLUS_4             0              23
  CLUS_5             2              37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  EOMES MUTATED        2      1      0      1      1
  EOMES WILD-TYPE     53     45     21     41     23
D7V10, multiclass
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  CLUS_1             2              53
  CLUS_2             1              45
  CLUS_3             0              21
  CLUS_4             1              41
  CLUS_5             1              23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        0      1      3      3
  PTEN WILD-TYPE     90     57     35     54
D8V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             90
  CLUS_2            1             57
  CLUS_3            3             35
  CLUS_4            3             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
  PTEN MUTATED        0      1      4      2
  PTEN WILD-TYPE     55     51     64     70
D8V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             55
  CLUS_2            1             51
  CLUS_3            4             64
  CLUS_4            2             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        1      1      1      1
  PTEN WILD-TYPE     55     41     54     56
D8V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             55
  CLUS_2            1             41
  CLUS_3            1             54
  CLUS_4            1             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
  PTEN MUTATED        1      0      1      1      0      1
  PTEN WILD-TYPE     22     34     46     61     22     21
D8V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             22
  CLUS_2            0             34
  CLUS_3            1             46
  CLUS_4            1             61
  CLUS_5            0             22
  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    109     68     61
D8V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1            109
  CLUS_2            4             68
  CLUS_3            2             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
  PTEN MUTATED        0      0      4      2      0      0      1
  PTEN WILD-TYPE     43     21     44     44     29     25     32
D8V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             43
  CLUS_2            0             21
  CLUS_3            4             44
  CLUS_4            2             44
  CLUS_5            0             29
  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     99     49     91
D8V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             99
  CLUS_2            1             49
  CLUS_3            5             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
  PTEN MUTATED        1      0      6      0
  PTEN WILD-TYPE     78     36    104     21
D8V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             78
  CLUS_2            0             36
  CLUS_3            6            104
  CLUS_4            0             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 CLUS_4 CLUS_5
  PTEN MUTATED        1      0      3      1      1
  PTEN WILD-TYPE     55     26     41     22     38
D8V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             55
  CLUS_2            0             26
  CLUS_3            3             41
  CLUS_4            1             22
  CLUS_5            1             38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        0      3      2      0      1
  PTEN WILD-TYPE     55     43     19     42     23
D8V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             55
  CLUS_2            3             43
  CLUS_3            2             19
  CLUS_4            0             42
  CLUS_5            1             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = KRTAP5-5 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        3      2      1      1
  KRTAP5-5 WILD-TYPE     87     56     37     56
D9V1, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                 87
  CLUS_2                2                 56
  CLUS_3                1                 37
  CLUS_4                1                 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
  KRTAP5-5 MUTATED        1      5      0      1
  KRTAP5-5 WILD-TYPE     54     47     68     71
D9V2, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 54
  CLUS_2                5                 47
  CLUS_3                0                 68
  CLUS_4                1                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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     53     40     55     56
D9V3, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                 53
  CLUS_2                2                 40
  CLUS_3                0                 55
  CLUS_4                1                 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
  KRTAP5-5 MUTATED        1      3      0      0      0      2
  KRTAP5-5 WILD-TYPE     22     31     47     62     22     20
D9V4, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 22
  CLUS_2                3                 31
  CLUS_3                0                 47
  CLUS_4                0                 62
  CLUS_5                0                 22
  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    107     72     59
D9V5, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                107
  CLUS_2                0                 72
  CLUS_3                4                 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
  KRTAP5-5 MUTATED        2      1      0      4      0      0      0
  KRTAP5-5 WILD-TYPE     41     20     48     42     29     25     33
D9V6, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                2                 41
  CLUS_2                1                 20
  CLUS_3                0                 48
  CLUS_4                4                 42
  CLUS_5                0                 29
  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     94     50     95
D9V7, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                6                 94
  CLUS_2                0                 50
  CLUS_3                1                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KRTAP5-5 MUTATED        5      0      1      1
  KRTAP5-5 WILD-TYPE     74     36    109     20
D9V8, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                5                 74
  CLUS_2                0                 36
  CLUS_3                1                109
  CLUS_4                1                 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 CLUS_4 CLUS_5
  KRTAP5-5 MUTATED        3      2      0      2      0
  KRTAP5-5 WILD-TYPE     53     24     44     21     39
D9V9, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                 53
  CLUS_2                2                 24
  CLUS_3                0                 44
  CLUS_4                2                 21
  CLUS_5                0                 39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KRTAP5-5 MUTATED        4      0      1      0      2
  KRTAP5-5 WILD-TYPE     51     46     20     42     22
D9V10, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                4                 51
  CLUS_2                0                 46
  CLUS_3                1                 20
  CLUS_4                0                 42
  CLUS_5                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = CABLES1 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CABLES1 MUTATED        1      1      0      1
  CABLES1 WILD-TYPE     89     57     38     56
D10V1, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                89
  CLUS_2               1                57
  CLUS_3               0                38
  CLUS_4               1                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
  CABLES1 MUTATED        0      1      2      0
  CABLES1 WILD-TYPE     55     51     66     72
D10V2, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               0                55
  CLUS_2               1                51
  CLUS_3               2                66
  CLUS_4               0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CABLES1 MUTATED        1      0      2      0
  CABLES1 WILD-TYPE     55     42     53     57
D10V3, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                55
  CLUS_2               0                42
  CLUS_3               2                53
  CLUS_4               0                57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     22     34     47     60     22     22
D10V4, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                22
  CLUS_2               0                34
  CLUS_3               0                47
  CLUS_4               2                60
  CLUS_5               0                22
  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    110     70     62
D10V5, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               0               110
  CLUS_2               2                70
  CLUS_3               1                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
  CABLES1 MUTATED        0      0      1      1      0      1      0
  CABLES1 WILD-TYPE     43     21     47     45     29     24     33
D10V6, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               0                43
  CLUS_2               0                21
  CLUS_3               1                47
  CLUS_4               1                45
  CLUS_5               0                29
  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     99     50     94
D10V7, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                99
  CLUS_2               0                50
  CLUS_3               2                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CABLES1 MUTATED        1      0      2      0
  CABLES1 WILD-TYPE     78     36    108     21
D10V8, multiclass
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  CLUS_1               1                78
  CLUS_2               0                36
  CLUS_3               2               108
  CLUS_4               0                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 CLUS_4 CLUS_5
  CABLES1 MUTATED        1      0      1      0      0
  CABLES1 WILD-TYPE     55     26     43     23     39
D10V9, multiclass
[1] "Remove cluster labels:" "CABLES1 MUTATED"       
clus
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                2               186 
       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-AB2L 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2O        TCGA-DX-AB2P        TCGA-DX-AB2Q        TCGA-DX-AB2S 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2T        TCGA-DX-AB2V        TCGA-DX-AB2W        TCGA-DX-AB2X 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2Z        TCGA-DX-AB30        TCGA-DX-AB32        TCGA-DX-AB35 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB36        TCGA-DX-AB37        TCGA-DX-AB3B        TCGA-DX-AB3C 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A3TO        TCGA-FX-A76Y        TCGA-FX-A8OO        TCGA-HB-A2OT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-HB-A5W3        TCGA-HS-A5N7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-HS-A5N8        TCGA-IE-A3OV        TCGA-IE-A4EH        TCGA-IE-A4EI 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IE-A4EJ        TCGA-IF-A4AJ        TCGA-IF-A4AK        TCGA-IS-A3K7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5        TCGA-IW-A3M6 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-JV-A5VE        TCGA-JV-A5VF        TCGA-JV-A75J        TCGA-K1-A3PN 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-K1-A3PO        TCGA-K1-A6RT        TCGA-K1-A6RU        TCGA-K1-A6RV 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-KD-A5QS        TCGA-KD-A5QT        TCGA-KD-A5QU        TCGA-KF-A41W 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-LI-A67I        TCGA-LI-A9QH        TCGA-MB-A5Y8        TCGA-MB-A5Y9 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MB-A5YA        TCGA-MB-A8JK        TCGA-MB-A8JL        TCGA-MJ-A68H 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MJ-A850        TCGA-MO-A47R        TCGA-PC-A5DK        TCGA-PC-A5DN 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-PC-A5DO        TCGA-PT-A8TR        TCGA-QC-A6FX        TCGA-QC-A7B5 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QC-AA9N        TCGA-QQ-A5VB        TCGA-QQ-A5VC        TCGA-QQ-A5VD 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QQ-A8VD        TCGA-QQ-A8VG        TCGA-QQ-A8VH        TCGA-RN-AAAQ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SG-A6Z4        TCGA-SG-A6Z7        TCGA-SG-A849        TCGA-SI-A71O 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SI-A71P        TCGA-SI-A71Q        TCGA-SI-AA8B        TCGA-SI-AA8C 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-UE-A6QU        TCGA-VT-A80J        TCGA-VT-AB3D        TCGA-WK-A8XO 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XQ        TCGA-WK-A8XS        TCGA-WK-A8XT        TCGA-WK-A8XX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XY        TCGA-WK-A8XZ        TCGA-WK-A8Y0        TCGA-WP-A9GB 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X2-A95T        TCGA-X6-A7W8        TCGA-X6-A7WC        TCGA-X6-A8C2 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X6-A8C3        TCGA-X6-A8C5        TCGA-X6-A8C6        TCGA-X6-A8C7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X9-A971        TCGA-X9-A973        TCGA-Z4-A8JB        TCGA-Z4-A9VC 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-Z4-AAPF        TCGA-Z4-AAPG 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CABLES1 MUTATED        1      1      0      0      0
  CABLES1 WILD-TYPE     54     45     21     42     24
D10V10, multiclass
[1] "Remove cluster labels:" "CABLES1 MUTATED"       
clus
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                2               186 
       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-AB2L 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2O        TCGA-DX-AB2P        TCGA-DX-AB2Q        TCGA-DX-AB2S 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2T        TCGA-DX-AB2V        TCGA-DX-AB2W        TCGA-DX-AB2X 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB2Z        TCGA-DX-AB30        TCGA-DX-AB32        TCGA-DX-AB35 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-DX-AB36        TCGA-DX-AB37        TCGA-DX-AB3B        TCGA-DX-AB3C 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-FX-A3TO        TCGA-FX-A76Y        TCGA-FX-A8OO        TCGA-HB-A2OT 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-HB-A5W3        TCGA-HS-A5N7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-HS-A5N8        TCGA-IE-A3OV        TCGA-IE-A4EH        TCGA-IE-A4EI 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IE-A4EJ        TCGA-IF-A4AJ        TCGA-IF-A4AK        TCGA-IS-A3K7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5        TCGA-IW-A3M6 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-JV-A5VE        TCGA-JV-A5VF        TCGA-JV-A75J        TCGA-K1-A3PN 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-K1-A3PO        TCGA-K1-A6RT        TCGA-K1-A6RU        TCGA-K1-A6RV 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-KD-A5QS        TCGA-KD-A5QT        TCGA-KD-A5QU        TCGA-KF-A41W 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-LI-A67I        TCGA-LI-A9QH        TCGA-MB-A5Y8        TCGA-MB-A5Y9 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MB-A5YA        TCGA-MB-A8JK        TCGA-MB-A8JL        TCGA-MJ-A68H 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-MJ-A850        TCGA-MO-A47R        TCGA-PC-A5DK        TCGA-PC-A5DN 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-PC-A5DO        TCGA-PT-A8TR        TCGA-QC-A6FX        TCGA-QC-A7B5 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QC-AA9N        TCGA-QQ-A5VB        TCGA-QQ-A5VC        TCGA-QQ-A5VD 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-QQ-A8VD        TCGA-QQ-A8VG        TCGA-QQ-A8VH        TCGA-RN-AAAQ 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SG-A6Z4        TCGA-SG-A6Z7        TCGA-SG-A849        TCGA-SI-A71O 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-SI-A71P        TCGA-SI-A71Q        TCGA-SI-AA8B        TCGA-SI-AA8C 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-UE-A6QU        TCGA-VT-A80J        TCGA-VT-AB3D        TCGA-WK-A8XO 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XQ        TCGA-WK-A8XS        TCGA-WK-A8XT        TCGA-WK-A8XX 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-WK-A8XY        TCGA-WK-A8XZ        TCGA-WK-A8Y0        TCGA-WP-A9GB 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X2-A95T        TCGA-X6-A7W8        TCGA-X6-A7WC        TCGA-X6-A8C2 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X6-A8C3        TCGA-X6-A8C5        TCGA-X6-A8C6        TCGA-X6-A8C7 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-X9-A971        TCGA-X9-A973        TCGA-Z4-A8JB        TCGA-Z4-A9VC 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 
       TCGA-Z4-AAPF        TCGA-Z4-AAPG 
"CABLES1 WILD-TYPE" "CABLES1 WILD-TYPE" 

Clustering(11) Variable = TRAF7 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRAF7 MUTATED        1      1      1      1
  TRAF7 WILD-TYPE     89     57     37     56
D11V1, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             1              89
  CLUS_2             1              57
  CLUS_3             1              37
  CLUS_4             1              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
  TRAF7 MUTATED        1      1      0      2
  TRAF7 WILD-TYPE     54     51     68     70
D11V2, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             1              54
  CLUS_2             1              51
  CLUS_3             0              68
  CLUS_4             2              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRAF7 MUTATED        2      1      0      1
  TRAF7 WILD-TYPE     54     41     55     56
D11V3, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              54
  CLUS_2             1              41
  CLUS_3             0              55
  CLUS_4             1              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
  TRAF7 MUTATED        2      1      1      0      0      0
  TRAF7 WILD-TYPE     21     33     46     62     22     22
D11V4, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             1              33
  CLUS_3             1              46
  CLUS_4             0              62
  CLUS_5             0              22
  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    107     72     62
D11V5, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             3             107
  CLUS_2             0              72
  CLUS_3             1              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
  TRAF7 MUTATED        2      0      0      0      0      0      2
  TRAF7 WILD-TYPE     41     21     48     46     29     25     31
D11V6, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              41
  CLUS_2             0              21
  CLUS_3             0              48
  CLUS_4             0              46
  CLUS_5             0              29
  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     98     49     95
D11V7, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              98
  CLUS_2             1              49
  CLUS_3             1              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TRAF7 MUTATED        2      0      2      0
  TRAF7 WILD-TYPE     77     36    108     21
D11V8, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             2              77
  CLUS_2             0              36
  CLUS_3             2             108
  CLUS_4             0              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 CLUS_4 CLUS_5
  TRAF7 MUTATED        0      2      0      1      0
  TRAF7 WILD-TYPE     56     24     44     22     39
D11V9, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             2              24
  CLUS_3             0              44
  CLUS_4             1              22
  CLUS_5             0              39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TRAF7 MUTATED        1      0      2      0      0
  TRAF7 WILD-TYPE     54     46     19     42     24
D11V10, multiclass
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  CLUS_1             1              54
  CLUS_2             0              46
  CLUS_3             2              19
  CLUS_4             0              42
  CLUS_5             0              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = LOR MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LOR MUTATED        1      4      1      0
  LOR WILD-TYPE     89     54     37     57
D12V1, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           1            89
  CLUS_2           4            54
  CLUS_3           1            37
  CLUS_4           0            57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        2      3      0      1
  LOR WILD-TYPE     53     49     68     71
D12V2, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           2            53
  CLUS_2           3            49
  CLUS_3           0            68
  CLUS_4           1            71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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     52     41     55     57
D12V3, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           4            52
  CLUS_2           1            41
  CLUS_3           0            55
  CLUS_4           0            57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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     22     31     47     62     22     21
D12V4, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           1            22
  CLUS_2           3            31
  CLUS_3           0            47
  CLUS_4           0            62
  CLUS_5           0            22
  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    106     71     62
D12V5, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           4           106
  CLUS_2           1            71
  CLUS_3           1            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
  LOR MUTATED        1      1      0      1      0      1      2
  LOR WILD-TYPE     42     20     48     45     29     24     31
D12V6, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           1            42
  CLUS_2           1            20
  CLUS_3           0            48
  CLUS_4           1            45
  CLUS_5           0            29
  CLUS_6           1            24
  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
  LOR MUTATED        5      0      1
  LOR WILD-TYPE     95     50     95
D12V7, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           5            95
  CLUS_2           0            50
  CLUS_3           1            95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LOR MUTATED        4      0      1      1
  LOR WILD-TYPE     75     36    109     20
D12V8, multiclass
        clus
vv       LOR MUTATED LOR WILD-TYPE
  CLUS_1           4            75
  CLUS_2           0            36
  CLUS_3           1           109
  CLUS_4           1            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 CLUS_4 CLUS_5
  LOR MUTATED        1      0      0      0      0
  LOR WILD-TYPE     55     26     44     23     39
D12V9, multiclass
[1] "Remove cluster labels:" "LOR MUTATED"           
clus
  LOR MUTATED LOR WILD-TYPE 
            1           187 
   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-AB2L    TCGA-DX-AB2O    TCGA-DX-AB2P    TCGA-DX-AB2Q    TCGA-DX-AB2S 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB2T    TCGA-DX-AB2V    TCGA-DX-AB2W    TCGA-DX-AB2X    TCGA-DX-AB2Z 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB30    TCGA-DX-AB32    TCGA-DX-AB35    TCGA-DX-AB36    TCGA-DX-AB37 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB3A    TCGA-DX-AB3B    TCGA-DX-AB3C    TCGA-FX-A2QS    TCGA-FX-A3NJ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-FX-A3NK    TCGA-FX-A3RE    TCGA-FX-A3TO    TCGA-FX-A76Y    TCGA-FX-A8OO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-HB-A2OT    TCGA-HB-A3YV    TCGA-HB-A43Z    TCGA-HB-A5W3    TCGA-HS-A5N7 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-HS-A5N8    TCGA-IE-A3OV    TCGA-IE-A4EH    TCGA-IE-A4EI    TCGA-IE-A4EJ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IF-A4AJ    TCGA-IF-A4AK    TCGA-IS-A3K7    TCGA-IS-A3KA    TCGA-IW-A3M4 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IW-A3M5    TCGA-IW-A3M6    TCGA-JV-A5VE    TCGA-JV-A5VF    TCGA-JV-A75J 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-K1-A3PN    TCGA-K1-A3PO    TCGA-K1-A6RT    TCGA-K1-A6RU    TCGA-K1-A6RV 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-KD-A5QS    TCGA-KD-A5QT    TCGA-KD-A5QU    TCGA-KF-A41W    TCGA-LI-A67I 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-LI-A9QH    TCGA-MB-A5Y8    TCGA-MB-A5Y9    TCGA-MB-A5YA    TCGA-MB-A8JK 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-MB-A8JL    TCGA-MJ-A68H    TCGA-MJ-A850    TCGA-MO-A47R    TCGA-PC-A5DK 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-PC-A5DN    TCGA-PC-A5DO    TCGA-PT-A8TR    TCGA-QC-A6FX    TCGA-QC-A7B5 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-QC-AA9N    TCGA-QQ-A5VB    TCGA-QQ-A5VC    TCGA-QQ-A5VD    TCGA-QQ-A8VD 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-QQ-A8VG    TCGA-QQ-A8VH    TCGA-RN-AAAQ    TCGA-SG-A6Z4    TCGA-SG-A6Z7 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-SG-A849    TCGA-SI-A71O    TCGA-SI-A71P    TCGA-SI-A71Q    TCGA-SI-AA8B 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-SI-AA8C    TCGA-UE-A6QU    TCGA-VT-A80J    TCGA-VT-AB3D    TCGA-WK-A8XO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-WK-A8XQ    TCGA-WK-A8XS    TCGA-WK-A8XT    TCGA-WK-A8XX    TCGA-WK-A8XY 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-WK-A8XZ    TCGA-WK-A8Y0    TCGA-WP-A9GB    TCGA-X2-A95T    TCGA-X6-A7W8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X6-A7WC    TCGA-X6-A8C2    TCGA-X6-A8C3    TCGA-X6-A8C5    TCGA-X6-A8C6 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X6-A8C7    TCGA-X9-A971    TCGA-X9-A973    TCGA-Z4-A8JB    TCGA-Z4-A9VC 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-Z4-AAPF    TCGA-Z4-AAPG 
"LOR WILD-TYPE" "LOR WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LOR MUTATED        1      0      0      0      0
  LOR WILD-TYPE     54     46     21     42     24
D12V10, multiclass
[1] "Remove cluster labels:" "LOR MUTATED"           
clus
  LOR MUTATED LOR WILD-TYPE 
            1           187 
   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-AB2L    TCGA-DX-AB2O    TCGA-DX-AB2P    TCGA-DX-AB2Q    TCGA-DX-AB2S 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB2T    TCGA-DX-AB2V    TCGA-DX-AB2W    TCGA-DX-AB2X    TCGA-DX-AB2Z 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB30    TCGA-DX-AB32    TCGA-DX-AB35    TCGA-DX-AB36    TCGA-DX-AB37 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-DX-AB3A    TCGA-DX-AB3B    TCGA-DX-AB3C    TCGA-FX-A2QS    TCGA-FX-A3NJ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-FX-A3NK    TCGA-FX-A3RE    TCGA-FX-A3TO    TCGA-FX-A76Y    TCGA-FX-A8OO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-HB-A2OT    TCGA-HB-A3YV    TCGA-HB-A43Z    TCGA-HB-A5W3    TCGA-HS-A5N7 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-HS-A5N8    TCGA-IE-A3OV    TCGA-IE-A4EH    TCGA-IE-A4EI    TCGA-IE-A4EJ 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IF-A4AJ    TCGA-IF-A4AK    TCGA-IS-A3K7    TCGA-IS-A3KA    TCGA-IW-A3M4 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-IW-A3M5    TCGA-IW-A3M6    TCGA-JV-A5VE    TCGA-JV-A5VF    TCGA-JV-A75J 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-K1-A3PN    TCGA-K1-A3PO    TCGA-K1-A6RT    TCGA-K1-A6RU    TCGA-K1-A6RV 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-KD-A5QS    TCGA-KD-A5QT    TCGA-KD-A5QU    TCGA-KF-A41W    TCGA-LI-A67I 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-LI-A9QH    TCGA-MB-A5Y8    TCGA-MB-A5Y9    TCGA-MB-A5YA    TCGA-MB-A8JK 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-MB-A8JL    TCGA-MJ-A68H    TCGA-MJ-A850    TCGA-MO-A47R    TCGA-PC-A5DK 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-PC-A5DN    TCGA-PC-A5DO    TCGA-PT-A8TR    TCGA-QC-A6FX    TCGA-QC-A7B5 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-QC-AA9N    TCGA-QQ-A5VB    TCGA-QQ-A5VC    TCGA-QQ-A5VD    TCGA-QQ-A8VD 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-QQ-A8VG    TCGA-QQ-A8VH    TCGA-RN-AAAQ    TCGA-SG-A6Z4    TCGA-SG-A6Z7 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-SG-A849    TCGA-SI-A71O    TCGA-SI-A71P    TCGA-SI-A71Q    TCGA-SI-AA8B 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-SI-AA8C    TCGA-UE-A6QU    TCGA-VT-A80J    TCGA-VT-AB3D    TCGA-WK-A8XO 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-WK-A8XQ    TCGA-WK-A8XS    TCGA-WK-A8XT    TCGA-WK-A8XX    TCGA-WK-A8XY 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-WK-A8XZ    TCGA-WK-A8Y0    TCGA-WP-A9GB    TCGA-X2-A95T    TCGA-X6-A7W8 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X6-A7WC    TCGA-X6-A8C2    TCGA-X6-A8C3    TCGA-X6-A8C5    TCGA-X6-A8C6 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-X6-A8C7    TCGA-X9-A971    TCGA-X9-A973    TCGA-Z4-A8JB    TCGA-Z4-A9VC 
"LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" "LOR WILD-TYPE" 
   TCGA-Z4-AAPF    TCGA-Z4-AAPG 
"LOR WILD-TYPE" "LOR WILD-TYPE" 

Clustering(13) Variable = R3HDM1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  R3HDM1 MUTATED        1      2      1      0
  R3HDM1 WILD-TYPE     89     56     37     57
D13V1, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              1               89
  CLUS_2              2               56
  CLUS_3              1               37
  CLUS_4              0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  R3HDM1 MUTATED        1      1      0      2
  R3HDM1 WILD-TYPE     54     51     68     70
D13V2, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              1               54
  CLUS_2              1               51
  CLUS_3              0               68
  CLUS_4              2               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  R3HDM1 MUTATED        2      0      1      0
  R3HDM1 WILD-TYPE     54     42     54     57
D13V3, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              2               54
  CLUS_2              0               42
  CLUS_3              1               54
  CLUS_4              0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  R3HDM1 MUTATED        0      1      1      0      0      1
  R3HDM1 WILD-TYPE     23     33     46     62     22     21
D13V4, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              0               23
  CLUS_2              1               33
  CLUS_3              1               46
  CLUS_4              0               62
  CLUS_5              0               22
  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
  R3HDM1 MUTATED        3      0      1
  R3HDM1 WILD-TYPE    107     72     62
D13V5, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              3              107
  CLUS_2              0               72
  CLUS_3              1               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
  R3HDM1 MUTATED        0      0      0      1      2      0      1
  R3HDM1 WILD-TYPE     43     21     48     45     27     25     32
D13V6, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              0               43
  CLUS_2              0               21
  CLUS_3              0               48
  CLUS_4              1               45
  CLUS_5              2               27
  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
  R3HDM1 MUTATED        2      0      1
  R3HDM1 WILD-TYPE     98     50     95
D13V7, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              2               98
  CLUS_2              0               50
  CLUS_3              1               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  R3HDM1 MUTATED        1      0      1      1
  R3HDM1 WILD-TYPE     78     36    109     20
D13V8, multiclass
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  CLUS_1              1               78
  CLUS_2              0               36
  CLUS_3              1              109
  CLUS_4              1               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 CLUS_4 CLUS_5
  R3HDM1 MUTATED        1      0      0      0      1
  R3HDM1 WILD-TYPE     55     26     44     23     38
D13V9, multiclass
[1] "Remove cluster labels:" "R3HDM1 MUTATED"        
clus
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               2              186 
      TCGA-3B-A9HI       TCGA-3B-A9HL       TCGA-3B-A9HP       TCGA-3B-A9HQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3B-A9HR       TCGA-3B-A9HS       TCGA-3B-A9HU       TCGA-3B-A9HX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3B-A9HY       TCGA-3B-A9HZ       TCGA-3B-A9I1       TCGA-3B-A9I3 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3R-A8YX       TCGA-DX-A1KU       TCGA-DX-A1KW       TCGA-DX-A1KX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A1KY       TCGA-DX-A1KZ       TCGA-DX-A1L0       TCGA-DX-A23R 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A23T       TCGA-DX-A23V       TCGA-DX-A240       TCGA-DX-A2IZ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A2J0       TCGA-DX-A2J1       TCGA-DX-A3LS       TCGA-DX-A3LW 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A3LY       TCGA-DX-A3M1       TCGA-DX-A3M2       TCGA-DX-A3U5 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A3U6       TCGA-DX-A3U7       TCGA-DX-A3U8       TCGA-DX-A3U9 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A3UA       TCGA-DX-A48K       TCGA-DX-A48L       TCGA-DX-A48N 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A48O       TCGA-DX-A6BA       TCGA-DX-A6BB       TCGA-DX-A6BE 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A6BF       TCGA-DX-A6YQ       TCGA-DX-A6YR       TCGA-DX-A6YU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A6YX       TCGA-DX-A6YZ       TCGA-DX-A7EI       TCGA-DX-A7EQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A7ES       TCGA-DX-A7ET       TCGA-DX-A7EU       TCGA-DX-A8BG 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BH       TCGA-DX-A8BJ       TCGA-DX-A8BK       TCGA-DX-A8BL 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BM       TCGA-DX-A8BN       TCGA-DX-A8BO       TCGA-DX-A8BP 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BQ       TCGA-DX-A8BR       TCGA-DX-A8BS       TCGA-DX-A8BT 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BU       TCGA-DX-A8BV       TCGA-DX-A8BX       TCGA-DX-AATS 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2F       TCGA-DX-AB2G       TCGA-DX-AB2J       TCGA-DX-AB2L 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2O       TCGA-DX-AB2P       TCGA-DX-AB2Q       TCGA-DX-AB2S 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2T       TCGA-DX-AB2V       TCGA-DX-AB2W       TCGA-DX-AB2X 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2Z       TCGA-DX-AB30       TCGA-DX-AB32       TCGA-DX-AB35 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB36       TCGA-DX-AB37       TCGA-DX-AB3A       TCGA-DX-AB3B 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB3C       TCGA-FX-A2QS       TCGA-FX-A3NJ       TCGA-FX-A3NK 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-FX-A3RE       TCGA-FX-A3TO       TCGA-FX-A76Y       TCGA-FX-A8OO 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-HB-A2OT       TCGA-HB-A3YV       TCGA-HB-A43Z       TCGA-HB-A5W3 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-HS-A5N7       TCGA-HS-A5N8       TCGA-IE-A3OV       TCGA-IE-A4EH 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IE-A4EI       TCGA-IE-A4EJ       TCGA-IF-A4AJ       TCGA-IF-A4AK 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IS-A3K7       TCGA-IS-A3KA       TCGA-IW-A3M4       TCGA-IW-A3M5 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IW-A3M6       TCGA-JV-A5VE       TCGA-JV-A5VF       TCGA-JV-A75J 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-K1-A3PN       TCGA-K1-A3PO       TCGA-K1-A6RT       TCGA-K1-A6RU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-K1-A6RV       TCGA-KD-A5QS       TCGA-KD-A5QT       TCGA-KD-A5QU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-KF-A41W       TCGA-LI-A67I       TCGA-LI-A9QH       TCGA-MB-A5Y8 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-MB-A5Y9       TCGA-MB-A5YA       TCGA-MB-A8JK       TCGA-MB-A8JL 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-MJ-A68H       TCGA-MJ-A850       TCGA-MO-A47R       TCGA-PC-A5DK 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-PC-A5DN       TCGA-PC-A5DO       TCGA-PT-A8TR       TCGA-QC-A6FX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-QC-AA9N       TCGA-QQ-A5VB       TCGA-QQ-A5VC       TCGA-QQ-A5VD 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-QQ-A8VD       TCGA-QQ-A8VG       TCGA-QQ-A8VH       TCGA-RN-AAAQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-SG-A6Z4       TCGA-SG-A6Z7       TCGA-SG-A849       TCGA-SI-A71O 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-SI-A71P       TCGA-SI-A71Q       TCGA-SI-AA8B       TCGA-SI-AA8C 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-UE-A6QU       TCGA-VT-A80J       TCGA-VT-AB3D       TCGA-WK-A8XO 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-WK-A8XQ       TCGA-WK-A8XS       TCGA-WK-A8XT       TCGA-WK-A8XX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-WK-A8XY       TCGA-WK-A8XZ       TCGA-WK-A8Y0       TCGA-WP-A9GB 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-X2-A95T       TCGA-X6-A7W8       TCGA-X6-A7WC       TCGA-X6-A8C2 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-X6-A8C3       TCGA-X6-A8C5       TCGA-X6-A8C6       TCGA-X6-A8C7 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-X9-A971       TCGA-X9-A973       TCGA-Z4-A8JB       TCGA-Z4-A9VC 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-Z4-AAPF       TCGA-Z4-AAPG 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  R3HDM1 MUTATED        0      0      0      1      1
  R3HDM1 WILD-TYPE     55     46     21     41     23
D13V10, multiclass
[1] "Remove cluster labels:" "R3HDM1 MUTATED"        
clus
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               2              186 
      TCGA-3B-A9HI       TCGA-3B-A9HL       TCGA-3B-A9HP       TCGA-3B-A9HQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3B-A9HR       TCGA-3B-A9HS       TCGA-3B-A9HU       TCGA-3B-A9HX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3B-A9HY       TCGA-3B-A9HZ       TCGA-3B-A9I1       TCGA-3B-A9I3 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-3R-A8YX       TCGA-DX-A1KU       TCGA-DX-A1KW       TCGA-DX-A1KX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A1KY       TCGA-DX-A1KZ       TCGA-DX-A1L0       TCGA-DX-A23R 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A23T       TCGA-DX-A23V       TCGA-DX-A240       TCGA-DX-A2IZ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A2J0       TCGA-DX-A2J1       TCGA-DX-A3LS       TCGA-DX-A3LW 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A3LY       TCGA-DX-A3M1       TCGA-DX-A3M2       TCGA-DX-A3U5 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A3U6       TCGA-DX-A3U7       TCGA-DX-A3U8       TCGA-DX-A3U9 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A3UA       TCGA-DX-A48K       TCGA-DX-A48L       TCGA-DX-A48N 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A48O       TCGA-DX-A6BA       TCGA-DX-A6BB       TCGA-DX-A6BE 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A6BF       TCGA-DX-A6YQ       TCGA-DX-A6YR       TCGA-DX-A6YU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A6YX       TCGA-DX-A6YZ       TCGA-DX-A7EI       TCGA-DX-A7EQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A7ES       TCGA-DX-A7ET       TCGA-DX-A7EU       TCGA-DX-A8BG 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BH       TCGA-DX-A8BJ       TCGA-DX-A8BK       TCGA-DX-A8BL 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BM       TCGA-DX-A8BN       TCGA-DX-A8BO       TCGA-DX-A8BP 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BQ       TCGA-DX-A8BR       TCGA-DX-A8BS       TCGA-DX-A8BT 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-A8BU       TCGA-DX-A8BV       TCGA-DX-A8BX       TCGA-DX-AATS 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2F       TCGA-DX-AB2G       TCGA-DX-AB2J       TCGA-DX-AB2L 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2O       TCGA-DX-AB2P       TCGA-DX-AB2Q       TCGA-DX-AB2S 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2T       TCGA-DX-AB2V       TCGA-DX-AB2W       TCGA-DX-AB2X 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB2Z       TCGA-DX-AB30       TCGA-DX-AB32       TCGA-DX-AB35 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB36       TCGA-DX-AB37       TCGA-DX-AB3A       TCGA-DX-AB3B 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-DX-AB3C       TCGA-FX-A2QS       TCGA-FX-A3NJ       TCGA-FX-A3NK 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-FX-A3RE       TCGA-FX-A3TO       TCGA-FX-A76Y       TCGA-FX-A8OO 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-HB-A2OT       TCGA-HB-A3YV       TCGA-HB-A43Z       TCGA-HB-A5W3 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-HS-A5N7       TCGA-HS-A5N8       TCGA-IE-A3OV       TCGA-IE-A4EH 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IE-A4EI       TCGA-IE-A4EJ       TCGA-IF-A4AJ       TCGA-IF-A4AK 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IS-A3K7       TCGA-IS-A3KA       TCGA-IW-A3M4       TCGA-IW-A3M5 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-IW-A3M6       TCGA-JV-A5VE       TCGA-JV-A5VF       TCGA-JV-A75J 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-K1-A3PN       TCGA-K1-A3PO       TCGA-K1-A6RT       TCGA-K1-A6RU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-K1-A6RV       TCGA-KD-A5QS       TCGA-KD-A5QT       TCGA-KD-A5QU 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-KF-A41W       TCGA-LI-A67I       TCGA-LI-A9QH       TCGA-MB-A5Y8 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-MB-A5Y9       TCGA-MB-A5YA       TCGA-MB-A8JK       TCGA-MB-A8JL 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-MJ-A68H       TCGA-MJ-A850       TCGA-MO-A47R       TCGA-PC-A5DK 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-PC-A5DN       TCGA-PC-A5DO       TCGA-PT-A8TR       TCGA-QC-A6FX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-QC-AA9N       TCGA-QQ-A5VB       TCGA-QQ-A5VC       TCGA-QQ-A5VD 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-QQ-A8VD       TCGA-QQ-A8VG       TCGA-QQ-A8VH       TCGA-RN-AAAQ 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-SG-A6Z4       TCGA-SG-A6Z7       TCGA-SG-A849       TCGA-SI-A71O 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-SI-A71P       TCGA-SI-A71Q       TCGA-SI-AA8B       TCGA-SI-AA8C 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-UE-A6QU       TCGA-VT-A80J       TCGA-VT-AB3D       TCGA-WK-A8XO 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-WK-A8XQ       TCGA-WK-A8XS       TCGA-WK-A8XT       TCGA-WK-A8XX 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-WK-A8XY       TCGA-WK-A8XZ       TCGA-WK-A8Y0       TCGA-WP-A9GB 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-X2-A95T       TCGA-X6-A7W8       TCGA-X6-A7WC       TCGA-X6-A8C2 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-X6-A8C3       TCGA-X6-A8C5       TCGA-X6-A8C6       TCGA-X6-A8C7 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-X9-A971       TCGA-X9-A973       TCGA-Z4-A8JB       TCGA-Z4-A9VC 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 
      TCGA-Z4-AAPF       TCGA-Z4-AAPG 
"R3HDM1 WILD-TYPE" "R3HDM1 WILD-TYPE" 

Clustering(14) Variable = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        5      4      0      0
  NF1 WILD-TYPE     85     54     38     57
D14V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5            85
  CLUS_2           4            54
  CLUS_3           0            38
  CLUS_4           0            57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        5      2      0      2
  NF1 WILD-TYPE     50     50     68     70
D14V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5            50
  CLUS_2           2            50
  CLUS_3           0            68
  CLUS_4           2            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        2      2      0      4
  NF1 WILD-TYPE     54     40     55     53
D14V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            54
  CLUS_2           2            40
  CLUS_3           0            55
  CLUS_4           4            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  NF1 MUTATED        0      1      3      0      0      4
  NF1 WILD-TYPE     23     33     44     62     22     18
D14V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            23
  CLUS_2           1            33
  CLUS_3           3            44
  CLUS_4           0            62
  CLUS_5           0            22
  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        5      0      4
  NF1 WILD-TYPE    105     72     59
D14V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5           105
  CLUS_2           0            72
  CLUS_3           4            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
  NF1 MUTATED        0      0      0      4      4      0      1
  NF1 WILD-TYPE     43     21     48     42     25     25     32
D14V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            43
  CLUS_2           0            21
  CLUS_3           0            48
  CLUS_4           4            42
  CLUS_5           4            25
  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      2      3
  NF1 WILD-TYPE     96     48     93
D14V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            96
  CLUS_2           2            48
  CLUS_3           3            93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        3      2      4      0
  NF1 WILD-TYPE     76     34    106     21
D14V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           3            76
  CLUS_2           2            34
  CLUS_3           4           106
  CLUS_4           0            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 CLUS_4 CLUS_5
  NF1 MUTATED        1      0      0      2      4
  NF1 WILD-TYPE     55     26     44     21     35
D14V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            55
  CLUS_2           0            26
  CLUS_3           0            44
  CLUS_4           2            21
  CLUS_5           4            35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NF1 MUTATED        0      0      2      4      1
  NF1 WILD-TYPE     55     46     19     38     23
D14V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           0            55
  CLUS_2           0            46
  CLUS_3           2            19
  CLUS_4           4            38
  CLUS_5           1            23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = COL4A3 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL4A3 MUTATED        0      2      2      0
  COL4A3 WILD-TYPE     90     56     36     57
D15V1, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              0               90
  CLUS_2              2               56
  CLUS_3              2               36
  CLUS_4              0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL4A3 MUTATED        0      2      1      1
  COL4A3 WILD-TYPE     55     50     67     71
D15V2, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              0               55
  CLUS_2              2               50
  CLUS_3              1               67
  CLUS_4              1               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL4A3 MUTATED        1      0      2      0
  COL4A3 WILD-TYPE     55     42     53     57
D15V3, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              1               55
  CLUS_2              0               42
  CLUS_3              2               53
  CLUS_4              0               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  COL4A3 MUTATED        0      1      0      1      0      1
  COL4A3 WILD-TYPE     23     33     47     61     22     21
D15V4, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              0               23
  CLUS_2              1               33
  CLUS_3              0               47
  CLUS_4              1               61
  CLUS_5              0               22
  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
  COL4A3 MUTATED        1      1      2
  COL4A3 WILD-TYPE    109     71     61
D15V5, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              1              109
  CLUS_2              1               71
  CLUS_3              2               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
  COL4A3 MUTATED        0      0      1      1      0      0      2
  COL4A3 WILD-TYPE     43     21     47     45     29     25     31
D15V6, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              0               43
  CLUS_2              0               21
  CLUS_3              1               47
  CLUS_4              1               45
  CLUS_5              0               29
  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
  COL4A3 MUTATED        3      0      1
  COL4A3 WILD-TYPE     97     50     95
D15V7, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              3               97
  CLUS_2              0               50
  CLUS_3              1               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  COL4A3 MUTATED        2      0      1      1
  COL4A3 WILD-TYPE     77     36    109     20
D15V8, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              2               77
  CLUS_2              0               36
  CLUS_3              1              109
  CLUS_4              1               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 CLUS_4 CLUS_5
  COL4A3 MUTATED        2      0      1      0      1
  COL4A3 WILD-TYPE     54     26     43     23     38
D15V9, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              2               54
  CLUS_2              0               26
  CLUS_3              1               43
  CLUS_4              0               23
  CLUS_5              1               38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  COL4A3 MUTATED        1      1      0      1      1
  COL4A3 WILD-TYPE     54     45     21     41     23
D15V10, multiclass
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  CLUS_1              1               54
  CLUS_2              1               45
  CLUS_3              0               21
  CLUS_4              1               41
  CLUS_5              1               23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = MEGF9 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEGF9 MUTATED        1      0      1      1
  MEGF9 WILD-TYPE     89     58     37     56
D16V1, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              89
  CLUS_2             0              58
  CLUS_3             1              37
  CLUS_4             1              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
  MEGF9 MUTATED        0      0      1      2
  MEGF9 WILD-TYPE     55     52     67     70
D16V2, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             0              55
  CLUS_2             0              52
  CLUS_3             1              67
  CLUS_4             2              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEGF9 MUTATED        0      0      1      0
  MEGF9 WILD-TYPE     56     42     54     57
D16V3, multiclass
[1] "Remove cluster labels:" "MEGF9 MUTATED"         
clus
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              1             209 
     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-AB2L 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2O      TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2T      TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2Z      TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB36      TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB3C      TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3RE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-FX-A3TO      TCGA-HB-A3L4      TCGA-HB-A3YV      TCGA-HB-A43Z 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-HB-A5W3      TCGA-HS-A5N7      TCGA-HS-A5N8      TCGA-IE-A3OV 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IE-A4EH      TCGA-IE-A4EI      TCGA-IE-A4EJ      TCGA-IE-A4EK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IE-A6BZ      TCGA-IS-A3K6      TCGA-IS-A3K7      TCGA-IS-A3K8 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-K1-A3PN      TCGA-K1-A3PO 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT      TCGA-K1-A6RU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-K1-A6RV      TCGA-KF-A41W      TCGA-LI-A67I      TCGA-LI-A9QH 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA      TCGA-MB-A8JK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-MB-A8JL      TCGA-MO-A47R      TCGA-N1-A6IA      TCGA-PC-A5DK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO      TCGA-PT-A8TR 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QC-A6FX      TCGA-QC-AA9N      TCGA-QQ-A5V2      TCGA-QQ-A5V9 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A5VA      TCGA-QQ-A5VB      TCGA-QQ-A5VC      TCGA-QQ-A5VD 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A8VG      TCGA-QQ-A8VH      TCGA-RN-A68Q      TCGA-RN-AAAQ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SG-A6Z4      TCGA-SG-A6Z7      TCGA-SG-A849      TCGA-SI-A71O 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SI-A71P      TCGA-SI-A71Q      TCGA-SI-AA8B      TCGA-SI-AA8C 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-UE-A6QT      TCGA-UE-A6QU      TCGA-VT-A80G      TCGA-VT-A80J 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X6-A7W8 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2      TCGA-X6-A8C3 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6      TCGA-X6-A8C7 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC      TCGA-Z4-AAPF 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-Z4-AAPG 
"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     23     34     47     62     22     21
D16V4, multiclass
[1] "Remove cluster labels:" "MEGF9 MUTATED"         
clus
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              1             209 
     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-AB2L 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2O      TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2T      TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB2Z      TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB36      TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-DX-AB3C      TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3RE 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-FX-A3TO      TCGA-HB-A3L4      TCGA-HB-A3YV      TCGA-HB-A43Z 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-HB-A5W3      TCGA-HS-A5N7      TCGA-HS-A5N8      TCGA-IE-A3OV 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IE-A4EH      TCGA-IE-A4EI      TCGA-IE-A4EJ      TCGA-IE-A4EK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IE-A6BZ      TCGA-IS-A3K6      TCGA-IS-A3K7      TCGA-IS-A3K8 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-K1-A3PN      TCGA-K1-A3PO 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT      TCGA-K1-A6RU 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-K1-A6RV      TCGA-KF-A41W      TCGA-LI-A67I      TCGA-LI-A9QH 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-MB-A5Y8      TCGA-MB-A5Y9      TCGA-MB-A5YA      TCGA-MB-A8JK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-MB-A8JL      TCGA-MO-A47R      TCGA-N1-A6IA      TCGA-PC-A5DK 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO      TCGA-PT-A8TR 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QC-A6FX      TCGA-QC-AA9N      TCGA-QQ-A5V2      TCGA-QQ-A5V9 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A5VA      TCGA-QQ-A5VB      TCGA-QQ-A5VC      TCGA-QQ-A5VD 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-QQ-A8VG      TCGA-QQ-A8VH      TCGA-RN-A68Q      TCGA-RN-AAAQ 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SG-A6Z4      TCGA-SG-A6Z7      TCGA-SG-A849      TCGA-SI-A71O 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-SI-A71P      TCGA-SI-A71Q      TCGA-SI-AA8B      TCGA-SI-AA8C 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-UE-A6QT      TCGA-UE-A6QU      TCGA-VT-A80G      TCGA-VT-A80J 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-WK-A8XX      TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X6-A7W8 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2      TCGA-X6-A8C3 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6      TCGA-X6-A8C7 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A9VC      TCGA-Z4-AAPF 
"MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" "MEGF9 WILD-TYPE" 
     TCGA-Z4-AAPG 
"MEGF9 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MEGF9 MUTATED        2      1      0
  MEGF9 WILD-TYPE    108     71     63
D16V5, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             2             108
  CLUS_2             1              71
  CLUS_3             0              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MEGF9 MUTATED        1      0      1      0      0      0      1
  MEGF9 WILD-TYPE     42     21     47     46     29     25     32
D16V6, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              42
  CLUS_2             0              21
  CLUS_3             1              47
  CLUS_4             0              46
  CLUS_5             0              29
  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        2      0      1
  MEGF9 WILD-TYPE     98     50     95
D16V7, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             2              98
  CLUS_2             0              50
  CLUS_3             1              95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MEGF9 MUTATED        2      0      1      0
  MEGF9 WILD-TYPE     77     36    109     21
D16V8, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             2              77
  CLUS_2             0              36
  CLUS_3             1             109
  CLUS_4             0              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 CLUS_4 CLUS_5
  MEGF9 MUTATED        0      1      1      0      1
  MEGF9 WILD-TYPE     56     25     43     23     38
D16V9, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             0              56
  CLUS_2             1              25
  CLUS_3             1              43
  CLUS_4             0              23
  CLUS_5             1              38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  MEGF9 MUTATED        1      1      0      1      0
  MEGF9 WILD-TYPE     54     45     21     41     24
D16V10, multiclass
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  CLUS_1             1              54
  CLUS_2             1              45
  CLUS_3             0              21
  CLUS_4             1              41
  CLUS_5             0              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = SCAP MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCAP MUTATED        0      2      1      0
  SCAP WILD-TYPE     90     56     37     57
D17V1, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            0             90
  CLUS_2            2             56
  CLUS_3            1             37
  CLUS_4            0             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCAP MUTATED        1      1      0      1
  SCAP WILD-TYPE     54     51     68     71
D17V2, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            1             54
  CLUS_2            1             51
  CLUS_3            0             68
  CLUS_4            1             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCAP MUTATED        2      0      1      0
  SCAP WILD-TYPE     54     42     54     57
D17V3, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            2             54
  CLUS_2            0             42
  CLUS_3            1             54
  CLUS_4            0             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  SCAP MUTATED        1      0      0      1      0      1
  SCAP WILD-TYPE     22     34     47     61     22     21
D17V4, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            1             22
  CLUS_2            0             34
  CLUS_3            0             47
  CLUS_4            1             61
  CLUS_5            0             22
  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
  SCAP MUTATED        2      0      1
  SCAP WILD-TYPE    108     72     62
D17V5, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            2            108
  CLUS_2            0             72
  CLUS_3            1             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
  SCAP MUTATED        0      0      0      1      1      0      1
  SCAP WILD-TYPE     43     21     48     45     28     25     32
D17V6, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            0             43
  CLUS_2            0             21
  CLUS_3            0             48
  CLUS_4            1             45
  CLUS_5            1             28
  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
  SCAP MUTATED        2      1      0
  SCAP WILD-TYPE     98     49     96
D17V7, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            2             98
  CLUS_2            1             49
  CLUS_3            0             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SCAP MUTATED        2      1      0      0
  SCAP WILD-TYPE     77     35    110     21
D17V8, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            2             77
  CLUS_2            1             35
  CLUS_3            0            110
  CLUS_4            0             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 CLUS_4 CLUS_5
  SCAP MUTATED        1      0      0      0      2
  SCAP WILD-TYPE     55     26     44     23     37
D17V9, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            1             55
  CLUS_2            0             26
  CLUS_3            0             44
  CLUS_4            0             23
  CLUS_5            2             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SCAP MUTATED        1      0      0      1      1
  SCAP WILD-TYPE     54     46     21     41     23
D17V10, multiclass
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  CLUS_1            1             54
  CLUS_2            0             46
  CLUS_3            0             21
  CLUS_4            1             41
  CLUS_5            1             23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
