[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTKIRC-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/KIRC-TP/11590644/KIRC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/10686177/transformed.cor.cli.txt"

nPatients in clinical file=537, in cluster file=491, common to both=417
[1]  29 417
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             44             373 
  SETD2 MUTATED SETD2 WILD-TYPE 
             44             373 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            41            376 
  BAP1 MUTATED BAP1 WILD-TYPE 
            41            376 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            18            399 
  PTEN MUTATED PTEN WILD-TYPE 
            18            399 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            136             281 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            136             281 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             26             391 
  KDM5C MUTATED KDM5C WILD-TYPE 
             26             391 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          166           251 
  VHL MUTATED VHL WILD-TYPE 
          166           251 
[1] "FAM200A MUTATION ANALYSIS"
[1] 3
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               412 
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               412 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             9            408 
  TP53 MUTATED TP53 WILD-TYPE 
             9            408 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             5            412 
  NEFH MUTATED NEFH WILD-TYPE 
             5            412 
[1] "CCDC120 MUTATION ANALYSIS"
[1] 3
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               413 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               413 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            23            394 
  MTOR MUTATED MTOR WILD-TYPE 
            23            394 
[1] "GUSB MUTATION ANALYSIS"
[1] 3
  GUSB MUTATED GUSB WILD-TYPE 
             4            413 
  GUSB MUTATED GUSB WILD-TYPE 
             4            413 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              405 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              405 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            412 
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            412 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              405 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              405 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           11           406 
  ATM MUTATED ATM WILD-TYPE 
           11           406 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             411 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             411 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             413 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             413 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             410 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             410 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
             4            413 
  RBMX MUTATED RBMX WILD-TYPE 
             4            413 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             414 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             414 
[1] "GPR172B MUTATION ANALYSIS"
[1] 3
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               413 
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               413 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             7            410 
  EGFR MUTATED EGFR WILD-TYPE 
             7            410 
[1] "IL1RAP MUTATION ANALYSIS"
[1] 3
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               4              413 
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               4              413 
[1] "BCL6 MUTATION ANALYSIS"
[1] 3
  BCL6 MUTATED BCL6 WILD-TYPE 
             5            412 
  BCL6 MUTATED BCL6 WILD-TYPE 
             5            412 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             411 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             411 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
              5             412 
  LARP1 MUTATED LARP1 WILD-TYPE 
              5             412 
[1] "KIAA1751 MUTATION ANALYSIS"
[1] 3
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                411 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                411 
[1] "INSRR MUTATION ANALYSIS"
[1] 3
  INSRR MUTATED INSRR WILD-TYPE 
              4             413 
  INSRR MUTATED INSRR WILD-TYPE 
              4             413 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 417 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 417 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=7, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SETD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        2      2      0
  SETD2 WILD-TYPE     20     19      3
D1V1, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             2              19
  CLUS_3             0               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  SETD2 MUTATED        1      2      0      0      1      0      0
  SETD2 WILD-TYPE      3      8      3     10      9      8      1
D1V2, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             1               3
  CLUS_2             2               8
  CLUS_3             0               3
  CLUS_4             0              10
  CLUS_5             1               9
  CLUS_6             0               8
  CLUS_7             0               1
[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
  SETD2 MUTATED       17     13     14
  SETD2 WILD-TYPE    173     82    116
D1V3, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            17             173
  CLUS_2            13              82
  CLUS_3            14             116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        6      0     22
  SETD2 WILD-TYPE     90     53     72
D1V4, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             6              90
  CLUS_2             0              53
  CLUS_3            22              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  SETD2 MUTATED       14      6      7      5      7      2
  SETD2 WILD-TYPE     79     50     60     59     61     36
D1V5, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            14              79
  CLUS_2             6              50
  CLUS_3             7              60
  CLUS_4             5              59
  CLUS_5             7              61
  CLUS_6             2              36
[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
  SETD2 MUTATED       14     14     13
  SETD2 WILD-TYPE     91    160     94
D1V6, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            14              91
  CLUS_2            14             160
  CLUS_3            13              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
  SETD2 MUTATED        8     15     21
  SETD2 WILD-TYPE     60    162    149
D1V7, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             8              60
  CLUS_2            15             162
  CLUS_3            21             149
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        6     24     14
  SETD2 WILD-TYPE    108    166     97
D1V8, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             6             108
  CLUS_2            24             166
  CLUS_3            14              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        7     17     18
  SETD2 WILD-TYPE     88    155    122
D1V9, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             7              88
  CLUS_2            17             155
  CLUS_3            18             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SETD2 MUTATED        7     11     18      6
  SETD2 WILD-TYPE    105     90    141     29
D1V10, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             7             105
  CLUS_2            11              90
  CLUS_3            18             141
  CLUS_4             6              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
  SETD2 MUTATED        0      3      7      3
  SETD2 WILD-TYPE     12     17     35     25
D1V11, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0              12
  CLUS_2             3              17
  CLUS_3             7              35
  CLUS_4             3              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SETD2 MUTATED        0      7      6
  SETD2 WILD-TYPE     14     38     37
D1V12, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0              14
  CLUS_2             7              38
  CLUS_3             6              37
[1] 3 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 = BAP1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        1      7      0
  BAP1 WILD-TYPE     21     14      3
D2V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            7             14
  CLUS_3            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  BAP1 MUTATED        0      0      0      7      1      0      0
  BAP1 WILD-TYPE      4     10      3      3      9      8      1
D2V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0             10
  CLUS_3            0              3
  CLUS_4            7              3
  CLUS_5            1              9
  CLUS_6            0              8
  CLUS_7            0              1
[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
  BAP1 MUTATED       11     10     20
  BAP1 WILD-TYPE    179     85    110
D2V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           11            179
  CLUS_2           10             85
  CLUS_3           20            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        1      6     16
  BAP1 WILD-TYPE     95     47     78
D2V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             95
  CLUS_2            6             47
  CLUS_3           16             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 CLUS_5 CLUS_6
  BAP1 MUTATED        4     10      8      2      9      2
  BAP1 WILD-TYPE     89     46     59     62     59     36
D2V5, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            4             89
  CLUS_2           10             46
  CLUS_3            8             59
  CLUS_4            2             62
  CLUS_5            9             59
  CLUS_6            2             36
[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
  BAP1 MUTATED       10      9     16
  BAP1 WILD-TYPE     95    165     91
D2V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           10             95
  CLUS_2            9            165
  CLUS_3           16             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
  BAP1 MUTATED        7      6     28
  BAP1 WILD-TYPE     61    171    142
D2V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            7             61
  CLUS_2            6            171
  CLUS_3           28            142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED       19      6     16
  BAP1 WILD-TYPE     95    184     95
D2V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           19             95
  CLUS_2            6            184
  CLUS_3           16             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
  BAP1 MUTATED        9      5     27
  BAP1 WILD-TYPE     86    167    113
D2V9, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            9             86
  CLUS_2            5            167
  CLUS_3           27            113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BAP1 MUTATED       11     20      4      6
  BAP1 WILD-TYPE    101     81    155     29
D2V10, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           11            101
  CLUS_2           20             81
  CLUS_3            4            155
  CLUS_4            6             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
  BAP1 MUTATED        2      1      1      4
  BAP1 WILD-TYPE     10     19     41     24
D2V11, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            2             10
  CLUS_2            1             19
  CLUS_3            1             41
  CLUS_4            4             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BAP1 MUTATED        2      4      2
  BAP1 WILD-TYPE     12     41     41
D2V12, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            2             12
  CLUS_2            4             41
  CLUS_3            2             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0      4      0
  PTEN WILD-TYPE     22     17      3
D3V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             22
  CLUS_2            4             17
  CLUS_3            0              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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      4      0      0      0      0      0
  PTEN WILD-TYPE      4      6      3     10     10      8      1
D3V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              4
  CLUS_2            4              6
  CLUS_3            0              3
  CLUS_4            0             10
  CLUS_5            0             10
  CLUS_6            0              8
  CLUS_7            0              1
[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        4      4      9
  PTEN WILD-TYPE    186     91    121
D3V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4            186
  CLUS_2            4             91
  CLUS_3            9            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        1      3      5
  PTEN WILD-TYPE     95     50     89
D3V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             95
  CLUS_2            3             50
  CLUS_3            5             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTEN MUTATED        2      7      2      2      4      1
  PTEN WILD-TYPE     91     49     65     62     64     37
D3V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             91
  CLUS_2            7             49
  CLUS_3            2             65
  CLUS_4            2             62
  CLUS_5            4             64
  CLUS_6            1             37
[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        3      7      8
  PTEN WILD-TYPE    102    167     99
D3V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3            102
  CLUS_2            7            167
  CLUS_3            8             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        2      0     16
  PTEN WILD-TYPE     66    177    154
D3V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             66
  CLUS_2            0            177
  CLUS_3           16            154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        4      2     12
  PTEN WILD-TYPE    110    188     99
D3V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4            110
  CLUS_2            2            188
  CLUS_3           12             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        7      1     10
  PTEN WILD-TYPE     88    171    130
D3V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7             88
  CLUS_2            1            171
  CLUS_3           10            130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger 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        7      5      3      3
  PTEN WILD-TYPE    105     96    156     32
D3V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            7            105
  CLUS_2            5             96
  CLUS_3            3            156
  CLUS_4            3             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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      0      0      3
  PTEN WILD-TYPE     12     20     42     25
D3V11, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             12
  CLUS_2            0             20
  CLUS_3            0             42
  CLUS_4            3             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        0      2      1
  PTEN WILD-TYPE     14     43     42
D3V12, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             14
  CLUS_2            2             43
  CLUS_3            1             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = PBRM1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED       10      4      1
  PBRM1 WILD-TYPE     12     17      2
D4V1, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            10              12
  CLUS_2             4              17
  CLUS_3             1               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PBRM1 MUTATED        2      4      0      0      4      4      1
  PBRM1 WILD-TYPE      2      6      3     10      6      4      0
D4V2, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             4               6
  CLUS_3             0               3
  CLUS_4             0              10
  CLUS_5             4               6
  CLUS_6             4               4
  CLUS_7             1               0
[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
  PBRM1 MUTATED       72     22     42
  PBRM1 WILD-TYPE    118     73     88
D4V3, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            72             118
  CLUS_2            22              73
  CLUS_3            42              88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED       42      6     42
  PBRM1 WILD-TYPE     54     47     52
D4V4, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            42              54
  CLUS_2             6              47
  CLUS_3            42              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PBRM1 MUTATED       47     16     21     19     13     10
  PBRM1 WILD-TYPE     46     40     46     45     55     28
D4V5, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            47              46
  CLUS_2            16              40
  CLUS_3            21              46
  CLUS_4            19              45
  CLUS_5            13              55
  CLUS_6            10              28
[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
  PBRM1 MUTATED       35     57     34
  PBRM1 WILD-TYPE     70    117     73
D4V6, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            35              70
  CLUS_2            57             117
  CLUS_3            34              73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED       14     71     50
  PBRM1 WILD-TYPE     54    106    120
D4V7, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            14              54
  CLUS_2            71             106
  CLUS_3            50             120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED       21     85     29
  PBRM1 WILD-TYPE     93    105     82
D4V8, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            21              93
  CLUS_2            85             105
  CLUS_3            29              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED       22     71     39
  PBRM1 WILD-TYPE     73    101    101
D4V9, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            22              73
  CLUS_2            71             101
  CLUS_3            39             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PBRM1 MUTATED       28     30     65      9
  PBRM1 WILD-TYPE     84     71     94     26
D4V10, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            28              84
  CLUS_2            30              71
  CLUS_3            65              94
  CLUS_4             9              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PBRM1 MUTATED        4      1     22      4
  PBRM1 WILD-TYPE      8     19     20     24
D4V11, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             4               8
  CLUS_2             1              19
  CLUS_3            22              20
  CLUS_4             4              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PBRM1 MUTATED        4      9     18
  PBRM1 WILD-TYPE     10     36     25
D4V12, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             4              10
  CLUS_2             9              36
  CLUS_3            18              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = KDM5C MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED        0      0      0
  KDM5C WILD-TYPE     22     21      3
D5V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KDM5C MUTATED        0      0      0      0      0      0      0
  KDM5C WILD-TYPE      4     10      3     10     10      8      1
D5V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED       12      3     11
  KDM5C WILD-TYPE    178     92    119
D5V3, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1            12             178
  CLUS_2             3              92
  CLUS_3            11             119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED        4      2     11
  KDM5C WILD-TYPE     92     51     83
D5V4, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             4              92
  CLUS_2             2              51
  CLUS_3            11              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  KDM5C MUTATED        5      7      5      2      3      1
  KDM5C WILD-TYPE     88     49     62     62     65     37
D5V5, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             5              88
  CLUS_2             7              49
  CLUS_3             5              62
  CLUS_4             2              62
  CLUS_5             3              65
  CLUS_6             1              37
[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
  KDM5C MUTATED       10      6      7
  KDM5C WILD-TYPE     95    168    100
D5V6, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1            10              95
  CLUS_2             6             168
  CLUS_3             7             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED        2      7     16
  KDM5C WILD-TYPE     66    170    154
D5V7, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             2              66
  CLUS_2             7             170
  CLUS_3            16             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED       11      7      7
  KDM5C WILD-TYPE    103    183    104
D5V8, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1            11             103
  CLUS_2             7             183
  CLUS_3             7             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED        2      8     16
  KDM5C WILD-TYPE     93    164    124
D5V9, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             2              93
  CLUS_2             8             164
  CLUS_3            16             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDM5C MUTATED        4     10      7      5
  KDM5C WILD-TYPE    108     91    152     30
D5V10, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             4             108
  CLUS_2            10              91
  CLUS_3             7             152
  CLUS_4             5              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDM5C MUTATED        0      0      2      1
  KDM5C WILD-TYPE     12     20     40     27
D5V11, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             0              12
  CLUS_2             0              20
  CLUS_3             2              40
  CLUS_4             1              27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  KDM5C MUTATED        0      2      1
  KDM5C WILD-TYPE     14     43     42
D5V12, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             0              14
  CLUS_2             2              43
  CLUS_3             1              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = VHL MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  VHL MUTATED       13      6      1
  VHL WILD-TYPE      9     15      2
D6V1, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          13             9
  CLUS_2           6            15
  CLUS_3           1             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  VHL MUTATED        2      2      0      4      6      5      1
  VHL WILD-TYPE      2      8      3      6      4      3      0
D6V2, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1           2             2
  CLUS_2           2             8
  CLUS_3           0             3
  CLUS_4           4             6
  CLUS_5           6             4
  CLUS_6           5             3
  CLUS_7           1             0
[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
  VHL MUTATED       80     40     46
  VHL WILD-TYPE    110     55     84
D6V3, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          80           110
  CLUS_2          40            55
  CLUS_3          46            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  VHL MUTATED       46     23     40
  VHL WILD-TYPE     50     30     54
D6V4, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          46            50
  CLUS_2          23            30
  CLUS_3          40            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  VHL MUTATED       47     21     21     22     26     18
  VHL WILD-TYPE     46     35     46     42     42     20
D6V5, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          47            46
  CLUS_2          21            35
  CLUS_3          21            46
  CLUS_4          22            42
  CLUS_5          26            42
  CLUS_6          18            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
  VHL MUTATED       39     77     39
  VHL WILD-TYPE     66     97     68
D6V6, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          39            66
  CLUS_2          77            97
  CLUS_3          39            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  VHL MUTATED       21     86     59
  VHL WILD-TYPE     47     91    111
D6V7, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          21            47
  CLUS_2          86            91
  CLUS_3          59           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  VHL MUTATED       38     88     40
  VHL WILD-TYPE     76    102     71
D6V8, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          38            76
  CLUS_2          88           102
  CLUS_3          40            71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  VHL MUTATED       39     76     47
  VHL WILD-TYPE     56     96     93
D6V9, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          39            56
  CLUS_2          76            96
  CLUS_3          47            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
  VHL MUTATED       45     33     73     11
  VHL WILD-TYPE     67     68     86     24
D6V10, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          45            67
  CLUS_2          33            68
  CLUS_3          73            86
  CLUS_4          11            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  VHL MUTATED        5      6     17     15
  VHL WILD-TYPE      7     14     25     13
D6V11, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1           5             7
  CLUS_2           6            14
  CLUS_3          17            25
  CLUS_4          15            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  VHL MUTATED        5     21     17
  VHL WILD-TYPE      9     24     26
D6V12, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1           5             9
  CLUS_2          21            24
  CLUS_3          17            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = FAM200A MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        2      0      0
  FAM200A WILD-TYPE     20     21      3
D7V1, multiclass
[1] "Remove cluster labels:" "FAM200A MUTATED"       
clus
  FAM200A MUTATED FAM200A WILD-TYPE 
                2                44 
       TCGA-A3-3308        TCGA-A3-3311        TCGA-A3-3316        TCGA-A3-3317 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3319        TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3455        TCGA-AK-3456        TCGA-AS-3778 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B8-4143 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4620        TCGA-BP-4161 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FAM200A MUTATED        0      0      0      0      2      0      0
  FAM200A WILD-TYPE      4     10      3     10      8      8      1
D7V2, multiclass
[1] "Remove cluster labels:" "FAM200A MUTATED"       
clus
  FAM200A MUTATED FAM200A WILD-TYPE 
                2                44 
       TCGA-A3-3308        TCGA-A3-3311        TCGA-A3-3316        TCGA-A3-3317 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3319        TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3455        TCGA-AK-3456        TCGA-AS-3778 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B8-4143 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4620        TCGA-BP-4161 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        2      2      1
  FAM200A WILD-TYPE    188     93    129
D7V3, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               2               188
  CLUS_2               2                93
  CLUS_3               1               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        0      0      1
  FAM200A WILD-TYPE     96     53     93
D7V4, multiclass
[1] "Remove cluster labels:" "FAM200A MUTATED"       
clus
  FAM200A MUTATED FAM200A WILD-TYPE 
                1               242 
       TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3367        TCGA-A3-3370 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-A3-3373        TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-AK-3425        TCGA-AK-3428        TCGA-AK-3431        TCGA-AK-3434 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-AK-3445        TCGA-AK-3450        TCGA-AK-3454        TCGA-AK-3458 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-AK-3460        TCGA-AK-3461        TCGA-B0-4690        TCGA-B0-4691 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4693        TCGA-B0-4694        TCGA-B0-4697        TCGA-B0-4700 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4703        TCGA-B0-4706        TCGA-B0-4707        TCGA-B0-4712 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4713        TCGA-B0-4714        TCGA-B0-4718        TCGA-B0-4810 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4813        TCGA-B0-4814        TCGA-B0-4815 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4818        TCGA-B0-4819 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4822        TCGA-B0-4823        TCGA-B0-4824        TCGA-B0-4827 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4828        TCGA-B0-4841        TCGA-B0-4842        TCGA-B0-4843 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4844        TCGA-B0-4845        TCGA-B0-4846        TCGA-B0-4847 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4848        TCGA-B0-4849        TCGA-B0-4852        TCGA-B0-4945 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5080        TCGA-B0-5092        TCGA-B0-5094        TCGA-B0-5095 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5096        TCGA-B0-5097        TCGA-B0-5099        TCGA-B0-5100 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5102        TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5108        TCGA-B0-5109        TCGA-B0-5110        TCGA-B0-5113 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5115        TCGA-B0-5116        TCGA-B0-5119        TCGA-B0-5120 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5121        TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5402 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5707        TCGA-B0-5709 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5713        TCGA-B0-5812 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4101        TCGA-B2-5633        TCGA-B2-5635 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B2-5641        TCGA-B4-5377        TCGA-B8-4146        TCGA-B8-4153 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4770        TCGA-BP-4782 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4801        TCGA-BP-4993        TCGA-BP-5010        TCGA-BP-5168 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5169        TCGA-BP-5170        TCGA-BP-5173        TCGA-BP-5174 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5175        TCGA-BP-5176        TCGA-BP-5177        TCGA-BP-5178 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5180        TCGA-BP-5182        TCGA-BP-5183        TCGA-BP-5184 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5185        TCGA-BP-5186        TCGA-BP-5187        TCGA-BP-5189 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5190        TCGA-BP-5191        TCGA-BP-5192        TCGA-BP-5194 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5195        TCGA-BP-5196        TCGA-BP-5198        TCGA-BP-5199 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5200        TCGA-BP-5201        TCGA-BP-5202        TCGA-CJ-4882 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4897        TCGA-CJ-4901        TCGA-CJ-4902        TCGA-CJ-4903 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4904        TCGA-CJ-4905        TCGA-CJ-4907        TCGA-CJ-4908 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4912        TCGA-CJ-4913        TCGA-CJ-4916        TCGA-CJ-4918 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4920        TCGA-CJ-4923        TCGA-CJ-5671        TCGA-CJ-5672 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-6027 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CW-5585        TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CW-6087        TCGA-CW-6090        TCGA-CW-6093        TCGA-CZ-4853 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-4865 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-4866        TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5454        TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5462        TCGA-CZ-5463        TCGA-CZ-5465        TCGA-CZ-5466 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5982        TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5987        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-EU-5906        TCGA-EU-5907 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  FAM200A MUTATED        0      0      0      0      0      3
  FAM200A WILD-TYPE     93     56     67     64     68     35
D7V5, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               0                93
  CLUS_2               0                56
  CLUS_3               0                67
  CLUS_4               0                64
  CLUS_5               0                68
  CLUS_6               3                35
[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
  FAM200A MUTATED        0      3      0
  FAM200A WILD-TYPE    105    171    107
D7V6, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               0               105
  CLUS_2               3               171
  CLUS_3               0               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        1      4      0
  FAM200A WILD-TYPE     67    173    170
D7V7, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               1                67
  CLUS_2               4               173
  CLUS_3               0               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        1      4      0
  FAM200A WILD-TYPE    113    186    111
D7V8, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               1               113
  CLUS_2               4               186
  CLUS_3               0               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        1      4      0
  FAM200A WILD-TYPE     94    168    140
D7V9, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               1                94
  CLUS_2               4               168
  CLUS_3               0               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM200A MUTATED        1      0      4      0
  FAM200A WILD-TYPE    111    101    155     35
D7V10, multiclass
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  CLUS_1               1               111
  CLUS_2               0               101
  CLUS_3               4               155
  CLUS_4               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FAM200A MUTATED        0      0      1      0
  FAM200A WILD-TYPE     12     20     41     28
D7V11, multiclass
[1] "Remove cluster labels:" "FAM200A MUTATED"       
clus
  FAM200A MUTATED FAM200A WILD-TYPE 
                1               101 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4700        TCGA-B0-4706        TCGA-B0-4712        TCGA-B0-4810 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4836        TCGA-B0-4837        TCGA-B0-4852 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5080        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5699        TCGA-B0-5702 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5709        TCGA-B2-3924        TCGA-B2-5633 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B2-5635        TCGA-B4-5377        TCGA-B8-4621        TCGA-B8-5545 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552        TCGA-B8-5553 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4173        TCGA-BP-4340        TCGA-BP-4761        TCGA-BP-4770 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4804 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4807        TCGA-BP-4961        TCGA-BP-4967        TCGA-BP-4968 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4970        TCGA-BP-4974        TCGA-BP-4976        TCGA-BP-4981 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4988        TCGA-BP-4989 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4992        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5001 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4870        TCGA-CJ-4875 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4895        TCGA-CJ-5671 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5681        TCGA-CJ-5683 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CW-5585 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4857 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5459        TCGA-CZ-5462        TCGA-CZ-5463 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5470 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5569 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-EU-5904 
"FAM200A WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  FAM200A MUTATED        0      0      1
  FAM200A WILD-TYPE     14     45     42
D7V12, multiclass
[1] "Remove cluster labels:" "FAM200A MUTATED"       
clus
  FAM200A MUTATED FAM200A WILD-TYPE 
                1               101 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4700        TCGA-B0-4706        TCGA-B0-4712        TCGA-B0-4810 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4836        TCGA-B0-4837        TCGA-B0-4852 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5080        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5399 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5699        TCGA-B0-5702 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5709        TCGA-B2-3924        TCGA-B2-5633 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B2-5635        TCGA-B4-5377        TCGA-B8-4621        TCGA-B8-5545 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552        TCGA-B8-5553 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4173        TCGA-BP-4340        TCGA-BP-4761        TCGA-BP-4770 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4804 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4807        TCGA-BP-4961        TCGA-BP-4967        TCGA-BP-4968 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4970        TCGA-BP-4974        TCGA-BP-4976        TCGA-BP-4981 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4988        TCGA-BP-4989 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-4992        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5001 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4870        TCGA-CJ-4875 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4895        TCGA-CJ-5671 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5681        TCGA-CJ-5683 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CW-5585 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4857 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5459        TCGA-CZ-5462        TCGA-CZ-5463 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5470 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5569 
"FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" "FAM200A WILD-TYPE" 
       TCGA-EU-5904 
"FAM200A WILD-TYPE" 

Clustering(8) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        0      0      0
  TP53 WILD-TYPE     22     21      3
D8V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  TP53 MUTATED        0      0      0      0      0      0      0
  TP53 WILD-TYPE      4     10      3     10     10      8      1
D8V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        3      1      5
  TP53 WILD-TYPE    187     94    125
D8V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3            187
  CLUS_2            1             94
  CLUS_3            5            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        1      2      3
  TP53 WILD-TYPE     95     51     91
D8V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             95
  CLUS_2            2             51
  CLUS_3            3             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 CLUS_5 CLUS_6
  TP53 MUTATED        0      2      2      1      2      1
  TP53 WILD-TYPE     93     54     65     63     66     37
D8V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             93
  CLUS_2            2             54
  CLUS_3            2             65
  CLUS_4            1             63
  CLUS_5            2             66
  CLUS_6            1             37
[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        1      3      4
  TP53 WILD-TYPE    104    171    103
D8V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1            104
  CLUS_2            3            171
  CLUS_3            4            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2      2      5
  TP53 WILD-TYPE     66    175    165
D8V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             66
  CLUS_2            2            175
  CLUS_3            5            165
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        2      2      5
  TP53 WILD-TYPE    112    188    106
D8V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2            112
  CLUS_2            2            188
  CLUS_3            5            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        3      2      4
  TP53 WILD-TYPE     92    170    136
D8V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             92
  CLUS_2            2            170
  CLUS_3            4            136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        4      2      2      1
  TP53 WILD-TYPE    108     99    157     34
D8V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4            108
  CLUS_2            2             99
  CLUS_3            2            157
  CLUS_4            1             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        0      1      2      1
  TP53 WILD-TYPE     12     19     40     27
D8V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             12
  CLUS_2            1             19
  CLUS_3            2             40
  CLUS_4            1             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        0      2      2
  TP53 WILD-TYPE     14     43     41
D8V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             14
  CLUS_2            2             43
  CLUS_3            2             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = NEFH MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        0      0      0
  NEFH WILD-TYPE     22     21      3
D9V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NEFH MUTATED        0      0      0      0      0      0      0
  NEFH WILD-TYPE      4     10      3     10     10      8      1
D9V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      1      1
  NEFH WILD-TYPE    187     94    129
D9V3, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3            187
  CLUS_2            1             94
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      0      1
  NEFH WILD-TYPE     93     53     93
D9V4, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             93
  CLUS_2            0             53
  CLUS_3            1             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 CLUS_5 CLUS_6
  NEFH MUTATED        2      0      1      1      1      0
  NEFH WILD-TYPE     91     56     66     63     67     38
D9V5, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            2             91
  CLUS_2            0             56
  CLUS_3            1             66
  CLUS_4            1             63
  CLUS_5            1             67
  CLUS_6            0             38
[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
  NEFH MUTATED        0      2      3
  NEFH WILD-TYPE    105    172    104
D9V6, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0            105
  CLUS_2            2            172
  CLUS_3            3            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      0      2
  NEFH WILD-TYPE     65    177    168
D9V7, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3             65
  CLUS_2            0            177
  CLUS_3            2            168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        3      1      1
  NEFH WILD-TYPE    111    189    110
D9V8, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            3            111
  CLUS_2            1            189
  CLUS_3            1            110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        0      3      2
  NEFH WILD-TYPE     95    169    138
D9V9, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0             95
  CLUS_2            3            169
  CLUS_3            2            138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        1      2      2      0
  NEFH WILD-TYPE    111     99    157     35
D9V10, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            1            111
  CLUS_2            2             99
  CLUS_3            2            157
  CLUS_4            0             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NEFH MUTATED        0      0      3      0
  NEFH WILD-TYPE     12     20     39     28
D9V11, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0             12
  CLUS_2            0             20
  CLUS_3            3             39
  CLUS_4            0             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  NEFH MUTATED        0      0      3
  NEFH WILD-TYPE     14     45     40
D9V12, multiclass
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  CLUS_1            0             14
  CLUS_2            0             45
  CLUS_3            3             40
[1] 3 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 = CCDC120 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        0      0      0
  CCDC120 WILD-TYPE     22     21      3
D10V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  CCDC120 MUTATED        0      0      0      0      0      0      0
  CCDC120 WILD-TYPE      4     10      3     10     10      8      1
D10V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        0      2      2
  CCDC120 WILD-TYPE    190     93    128
D10V3, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               0               190
  CLUS_2               2                93
  CLUS_3               2               128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        0      1      1
  CCDC120 WILD-TYPE     96     52     93
D10V4, multiclass
[1] "Remove cluster labels:" "CCDC120 MUTATED"       
clus
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                2               241 
       TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3367        TCGA-A3-3370 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-A3-3373        TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-AK-3428        TCGA-AK-3431        TCGA-AK-3434        TCGA-AK-3445 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-AK-3450        TCGA-AK-3454        TCGA-AK-3458        TCGA-AK-3460 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-AK-3461        TCGA-B0-4690        TCGA-B0-4691        TCGA-B0-4693 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4694        TCGA-B0-4697        TCGA-B0-4700        TCGA-B0-4703 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4706        TCGA-B0-4707        TCGA-B0-4710        TCGA-B0-4712 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4713        TCGA-B0-4714        TCGA-B0-4718        TCGA-B0-4810 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4813        TCGA-B0-4814        TCGA-B0-4815 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4818        TCGA-B0-4819 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4822        TCGA-B0-4823        TCGA-B0-4824        TCGA-B0-4827 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4828        TCGA-B0-4841        TCGA-B0-4842        TCGA-B0-4843 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4844        TCGA-B0-4845        TCGA-B0-4846        TCGA-B0-4847 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4848        TCGA-B0-4849        TCGA-B0-4852        TCGA-B0-4945 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5080        TCGA-B0-5092        TCGA-B0-5094        TCGA-B0-5095 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5096        TCGA-B0-5097        TCGA-B0-5099        TCGA-B0-5100 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5102        TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5108        TCGA-B0-5109        TCGA-B0-5110        TCGA-B0-5113 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5115        TCGA-B0-5116        TCGA-B0-5119        TCGA-B0-5120 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5121        TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5402 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5707        TCGA-B0-5709 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5713        TCGA-B0-5812 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4101        TCGA-B2-5633        TCGA-B2-5635 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B2-5641        TCGA-B4-5377        TCGA-B8-4146        TCGA-B8-4153 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4770        TCGA-BP-4782 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4801        TCGA-BP-4993        TCGA-BP-5010        TCGA-BP-5168 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5169        TCGA-BP-5170        TCGA-BP-5173        TCGA-BP-5174 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5175        TCGA-BP-5176        TCGA-BP-5177        TCGA-BP-5178 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5180        TCGA-BP-5182        TCGA-BP-5183        TCGA-BP-5184 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5185        TCGA-BP-5186        TCGA-BP-5187        TCGA-BP-5189 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5190        TCGA-BP-5191        TCGA-BP-5192        TCGA-BP-5194 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5195        TCGA-BP-5196        TCGA-BP-5198        TCGA-BP-5199 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5200        TCGA-BP-5201        TCGA-BP-5202        TCGA-CJ-4882 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4897        TCGA-CJ-4901        TCGA-CJ-4902        TCGA-CJ-4903 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4904        TCGA-CJ-4905        TCGA-CJ-4907        TCGA-CJ-4908 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4912        TCGA-CJ-4913        TCGA-CJ-4916        TCGA-CJ-4918 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4920        TCGA-CJ-4923        TCGA-CJ-5671        TCGA-CJ-5672 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-6027 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CW-5585        TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CW-6087        TCGA-CW-6090        TCGA-CW-6093        TCGA-CZ-4853 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-4865 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-4866        TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5454        TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5462        TCGA-CZ-5463        TCGA-CZ-5465        TCGA-CZ-5466 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5982 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5987 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-EU-5907 
"CCDC120 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  CCDC120 MUTATED        1      0      2      0      0      0
  CCDC120 WILD-TYPE     92     56     65     64     68     38
D10V5, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               1                92
  CLUS_2               0                56
  CLUS_3               2                65
  CLUS_4               0                64
  CLUS_5               0                68
  CLUS_6               0                38
[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
  CCDC120 MUTATED        1      1      1
  CCDC120 WILD-TYPE    104    173    106
D10V6, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               1               104
  CLUS_2               1               173
  CLUS_3               1               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        1      1      2
  CCDC120 WILD-TYPE     67    176    168
D10V7, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               1                67
  CLUS_2               1               176
  CLUS_3               2               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        0      3      1
  CCDC120 WILD-TYPE    114    187    110
D10V8, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               0               114
  CLUS_2               3               187
  CLUS_3               1               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        1      1      2
  CCDC120 WILD-TYPE     94    171    138
D10V9, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               1                94
  CLUS_2               1               171
  CLUS_3               2               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC120 MUTATED        1      1      2      0
  CCDC120 WILD-TYPE    111    100    157     35
D10V10, multiclass
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  CLUS_1               1               111
  CLUS_2               1               100
  CLUS_3               2               157
  CLUS_4               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CCDC120 MUTATED        0      0      0      2
  CCDC120 WILD-TYPE     12     20     42     26
D10V11, multiclass
[1] "Remove cluster labels:" "CCDC120 MUTATED"       
clus
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                2               100 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4700        TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4836        TCGA-B0-4837 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5080        TCGA-B0-5085        TCGA-B0-5088 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5699 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5705        TCGA-B0-5709        TCGA-B2-3924 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B2-5633        TCGA-B2-5635        TCGA-B4-5377        TCGA-B8-4621 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5545        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4340        TCGA-BP-4761 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4770        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4961        TCGA-BP-4967 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4970        TCGA-BP-4974        TCGA-BP-4976 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4988 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4989        TCGA-BP-4992        TCGA-BP-4995        TCGA-BP-4998 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4870 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4875        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4895        TCGA-CJ-5671 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5681        TCGA-CJ-5683 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CW-5585 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4857 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5459        TCGA-CZ-5462        TCGA-CZ-5463 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5989 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5569        TCGA-EU-5904 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  CCDC120 MUTATED        0      0      2
  CCDC120 WILD-TYPE     14     45     41
D10V12, multiclass
[1] "Remove cluster labels:" "CCDC120 MUTATED"       
clus
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                2               100 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4700        TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4836        TCGA-B0-4837 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5080        TCGA-B0-5085        TCGA-B0-5088 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5699 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5705        TCGA-B0-5709        TCGA-B2-3924 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B2-5633        TCGA-B2-5635        TCGA-B4-5377        TCGA-B8-4621 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5545        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4340        TCGA-BP-4761 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4770        TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4804        TCGA-BP-4807        TCGA-BP-4961        TCGA-BP-4967 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4970        TCGA-BP-4974        TCGA-BP-4976 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4981        TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4988 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-4989        TCGA-BP-4992        TCGA-BP-4995        TCGA-BP-4998 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-BP-5001        TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4870 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4875        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4895        TCGA-CJ-5671 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5681        TCGA-CJ-5683 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CW-5585 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4857 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5459        TCGA-CZ-5462        TCGA-CZ-5463 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5989 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5569        TCGA-EU-5904 
"CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" "CCDC120 WILD-TYPE" 

Clustering(11) Variable = MTOR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTOR MUTATED        1      1      0
  MTOR WILD-TYPE     21     20      3
D11V1, multiclass
[1] "Remove cluster labels:" "MTOR MUTATED"          
clus
  MTOR MUTATED MTOR WILD-TYPE 
             2             44 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3349     TCGA-A3-3362 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3372     TCGA-A3-3378 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3383     TCGA-AK-3444 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-AK-3455     TCGA-AK-3456     TCGA-AS-3778     TCGA-B2-3924 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-B2-4098     TCGA-B2-4099     TCGA-B8-4143     TCGA-B8-4148 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  MTOR MUTATED        0      0      0      1      1      0      0
  MTOR WILD-TYPE      4     10      3      9      9      8      1
D11V2, multiclass
[1] "Remove cluster labels:" "MTOR MUTATED"          
clus
  MTOR MUTATED MTOR WILD-TYPE 
             2             44 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3349     TCGA-A3-3362 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3372     TCGA-A3-3378 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3383     TCGA-AK-3444 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-AK-3455     TCGA-AK-3456     TCGA-AS-3778     TCGA-B2-3924 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-B2-4098     TCGA-B2-4099     TCGA-B8-4143     TCGA-B8-4148 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643 
"MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" "MTOR WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTOR MUTATED        9      5      9
  MTOR WILD-TYPE    181     90    121
D11V3, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            9            181
  CLUS_2            5             90
  CLUS_3            9            121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTOR MUTATED        5      2     11
  MTOR WILD-TYPE     91     51     83
D11V4, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            5             91
  CLUS_2            2             51
  CLUS_3           11             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 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
  MTOR MUTATED        4      8      8      0      1      0
  MTOR WILD-TYPE     89     48     59     64     67     38
D11V5, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            4             89
  CLUS_2            8             48
  CLUS_3            8             59
  CLUS_4            0             64
  CLUS_5            1             67
  CLUS_6            0             38
[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
  MTOR MUTATED        8      2     11
  MTOR WILD-TYPE     97    172     96
D11V6, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            8             97
  CLUS_2            2            172
  CLUS_3           11             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
  MTOR MUTATED        4      9     10
  MTOR WILD-TYPE     64    168    160
D11V7, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            4             64
  CLUS_2            9            168
  CLUS_3           10            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTOR MUTATED        7      9      7
  MTOR WILD-TYPE    107    181    104
D11V8, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            7            107
  CLUS_2            9            181
  CLUS_3            7            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTOR MUTATED        6      6     11
  MTOR WILD-TYPE     89    166    129
D11V9, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            6             89
  CLUS_2            6            166
  CLUS_3           11            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MTOR MUTATED        7      8      5      3
  MTOR WILD-TYPE    105     93    154     32
D11V10, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            7            105
  CLUS_2            8             93
  CLUS_3            5            154
  CLUS_4            3             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MTOR MUTATED        1      1      3      1
  MTOR WILD-TYPE     11     19     39     27
D11V11, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            1             11
  CLUS_2            1             19
  CLUS_3            3             39
  CLUS_4            1             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  MTOR MUTATED        1      3      2
  MTOR WILD-TYPE     13     42     41
D11V12, multiclass
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  CLUS_1            1             13
  CLUS_2            3             42
  CLUS_3            2             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = GUSB MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        0      0      0
  GUSB WILD-TYPE     22     21      3
D12V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GUSB MUTATED        0      0      0      0      0      0      0
  GUSB WILD-TYPE      4     10      3     10     10      8      1
D12V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        3      0      1
  GUSB WILD-TYPE    187     95    129
D12V3, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            3            187
  CLUS_2            0             95
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        0      0      2
  GUSB WILD-TYPE     96     53     92
D12V4, multiclass
[1] "Remove cluster labels:" "GUSB MUTATED"          
clus
  GUSB MUTATED GUSB WILD-TYPE 
             2            241 
    TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3367     TCGA-A3-3370 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-A3-3373     TCGA-A3-3376     TCGA-A3-3385     TCGA-A3-3387 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3428     TCGA-AK-3431     TCGA-AK-3434 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3450     TCGA-AK-3454     TCGA-AK-3458 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-AK-3460     TCGA-AK-3461     TCGA-B0-4690     TCGA-B0-4691 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4693     TCGA-B0-4694     TCGA-B0-4697     TCGA-B0-4700 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4706     TCGA-B0-4707     TCGA-B0-4710 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4712     TCGA-B0-4713     TCGA-B0-4714     TCGA-B0-4718 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4813     TCGA-B0-4814 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4815     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4818 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4819     TCGA-B0-4822     TCGA-B0-4823     TCGA-B0-4824 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4827     TCGA-B0-4828     TCGA-B0-4841     TCGA-B0-4842 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4843     TCGA-B0-4844     TCGA-B0-4845     TCGA-B0-4846 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4847     TCGA-B0-4848     TCGA-B0-4849     TCGA-B0-4852 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4945     TCGA-B0-5080     TCGA-B0-5092     TCGA-B0-5094 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5099     TCGA-B0-5100 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5102     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5402 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5698 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5709 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5711     TCGA-B0-5713     TCGA-B0-5812 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B2-3924     TCGA-B2-4101     TCGA-B2-5633     TCGA-B2-5635 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B2-5641     TCGA-B4-5377     TCGA-B8-4146     TCGA-B8-4153 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-5552     TCGA-B8-5553     TCGA-BP-4770     TCGA-BP-4782 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4801     TCGA-BP-4993     TCGA-BP-5010     TCGA-BP-5168 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5169     TCGA-BP-5170     TCGA-BP-5173     TCGA-BP-5174 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5175     TCGA-BP-5176     TCGA-BP-5177     TCGA-BP-5178 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5180     TCGA-BP-5182     TCGA-BP-5183     TCGA-BP-5184 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5185     TCGA-BP-5186     TCGA-BP-5187     TCGA-BP-5189 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5190     TCGA-BP-5191     TCGA-BP-5192     TCGA-BP-5194 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5195     TCGA-BP-5196     TCGA-BP-5198     TCGA-BP-5199 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5200     TCGA-BP-5201     TCGA-BP-5202     TCGA-CJ-4882 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4897     TCGA-CJ-4901     TCGA-CJ-4903     TCGA-CJ-4904 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4905     TCGA-CJ-4907     TCGA-CJ-4908     TCGA-CJ-4912 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4913     TCGA-CJ-4916     TCGA-CJ-4918     TCGA-CJ-4920 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4923     TCGA-CJ-5671     TCGA-CJ-5672     TCGA-CJ-5675 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-5676     TCGA-CJ-5677     TCGA-CJ-5678     TCGA-CJ-5679 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-5680     TCGA-CJ-5681     TCGA-CJ-5682     TCGA-CJ-5683 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-5684     TCGA-CJ-5686     TCGA-CJ-6027     TCGA-CJ-6028 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-6030     TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CJ-6033 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CW-5580     TCGA-CW-5581     TCGA-CW-5583     TCGA-CW-5585 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CW-5588     TCGA-CW-5589     TCGA-CW-5591     TCGA-CW-6087 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CW-6090     TCGA-CW-6093     TCGA-CZ-4853     TCGA-CZ-4856 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-4865     TCGA-CZ-4866 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5455     TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5459     TCGA-CZ-5460     TCGA-CZ-5461     TCGA-CZ-5462 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5463     TCGA-CZ-5465     TCGA-CZ-5466     TCGA-CZ-5467 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5468     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5982 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5987 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5988     TCGA-CZ-5989     TCGA-DV-5565     TCGA-DV-5566 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-EU-5907 
"GUSB WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GUSB MUTATED        0      0      1      0      2      0
  GUSB WILD-TYPE     93     56     66     64     66     38
D12V5, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            0             93
  CLUS_2            0             56
  CLUS_3            1             66
  CLUS_4            0             64
  CLUS_5            2             66
  CLUS_6            0             38
[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
  GUSB MUTATED        1      2      0
  GUSB WILD-TYPE    104    172    107
D12V6, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            1            104
  CLUS_2            2            172
  CLUS_3            0            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        1      0      3
  GUSB WILD-TYPE     67    177    167
D12V7, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            1             67
  CLUS_2            0            177
  CLUS_3            3            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        1      1      2
  GUSB WILD-TYPE    113    189    109
D12V8, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            1            113
  CLUS_2            1            189
  CLUS_3            2            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        2      1      1
  GUSB WILD-TYPE     93    171    139
D12V9, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            2             93
  CLUS_2            1            171
  CLUS_3            1            139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GUSB MUTATED        2      1      1      0
  GUSB WILD-TYPE    110    100    158     35
D12V10, multiclass
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  CLUS_1            2            110
  CLUS_2            1            100
  CLUS_3            1            158
  CLUS_4            0             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GUSB MUTATED        0      0      0      0
  GUSB WILD-TYPE     12     20     42     28
D12V11, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  GUSB MUTATED        0      0      0
  GUSB WILD-TYPE     14     45     43
D12V12, multiclass

Clustering(13) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        0      0      0
  PIK3CA WILD-TYPE     22     21      3
D13V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PIK3CA MUTATED        0      0      0      0      0      0      0
  PIK3CA WILD-TYPE      4     10      3     10     10      8      1
D13V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        7      1      4
  PIK3CA WILD-TYPE    183     94    126
D13V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7              183
  CLUS_2              1               94
  CLUS_3              4              126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        3      0      3
  PIK3CA WILD-TYPE     93     53     91
D13V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               93
  CLUS_2              0               53
  CLUS_3              3               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 CLUS_5 CLUS_6
  PIK3CA MUTATED        4      1      1      2      3      0
  PIK3CA WILD-TYPE     89     55     66     62     65     38
D13V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               89
  CLUS_2              1               55
  CLUS_3              1               66
  CLUS_4              2               62
  CLUS_5              3               65
  CLUS_6              0               38
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        5      3      3
  PIK3CA WILD-TYPE    100    171    104
D13V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5              100
  CLUS_2              3              171
  CLUS_3              3              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        0      6      6
  PIK3CA WILD-TYPE     68    171    164
D13V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               68
  CLUS_2              6              171
  CLUS_3              6              164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        2      5      5
  PIK3CA WILD-TYPE    112    185    106
D13V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2              112
  CLUS_2              5              185
  CLUS_3              5              106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        3      4      5
  PIK3CA WILD-TYPE     92    168    135
D13V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               92
  CLUS_2              4              168
  CLUS_3              5              135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        4      2      5      1
  PIK3CA WILD-TYPE    108     99    154     34
D13V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4              108
  CLUS_2              2               99
  CLUS_3              5              154
  CLUS_4              1               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        0      0      0      0
  PIK3CA WILD-TYPE     12     20     42     28
D13V11, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        0      0      0
  PIK3CA WILD-TYPE     14     45     43
D13V12, multiclass

Clustering(14) Variable = PCK1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        1      0      0
  PCK1 WILD-TYPE     21     21      3
D14V1, multiclass
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             45 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3346     TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3362 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3372     TCGA-A3-3378 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3383     TCGA-AK-3444 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AK-3455     TCGA-AK-3456     TCGA-AS-3778     TCGA-B2-3924 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B2-4098     TCGA-B2-4099     TCGA-B8-4143     TCGA-B8-4148 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CJ-4644 
"PCK1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PCK1 MUTATED        1      0      0      0      0      0      0
  PCK1 WILD-TYPE      3     10      3     10     10      8      1
D14V2, multiclass
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             45 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3346     TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3362 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3372     TCGA-A3-3378 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3383     TCGA-AK-3444 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AK-3455     TCGA-AK-3456     TCGA-AS-3778     TCGA-B2-3924 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B2-4098     TCGA-B2-4099     TCGA-B8-4143     TCGA-B8-4148 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CJ-4644 
"PCK1 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        4      0      1
  PCK1 WILD-TYPE    186     95    129
D14V3, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            4            186
  CLUS_2            0             95
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        1      0      2
  PCK1 WILD-TYPE     95     53     92
D14V4, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            1             95
  CLUS_2            0             53
  CLUS_3            2             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 CLUS_5 CLUS_6
  PCK1 MUTATED        1      0      1      1      1      0
  PCK1 WILD-TYPE     92     56     66     63     67     38
D14V5, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            1             92
  CLUS_2            0             56
  CLUS_3            1             66
  CLUS_4            1             63
  CLUS_5            1             67
  CLUS_6            0             38
[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
  PCK1 MUTATED        1      1      2
  PCK1 WILD-TYPE    104    173    105
D14V6, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            1            104
  CLUS_2            1            173
  CLUS_3            2            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        0      3      2
  PCK1 WILD-TYPE     68    174    168
D14V7, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            0             68
  CLUS_2            3            174
  CLUS_3            2            168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        0      3      2
  PCK1 WILD-TYPE    114    187    109
D14V8, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            0            114
  CLUS_2            3            187
  CLUS_3            2            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        2      2      1
  PCK1 WILD-TYPE     93    170    139
D14V9, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            2             93
  CLUS_2            2            170
  CLUS_3            1            139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCK1 MUTATED        3      0      2      0
  PCK1 WILD-TYPE    109    101    157     35
D14V10, multiclass
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  CLUS_1            3            109
  CLUS_2            0            101
  CLUS_3            2            157
  CLUS_4            0             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PCK1 MUTATED        0      0      0      0
  PCK1 WILD-TYPE     12     20     42     28
D14V11, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PCK1 MUTATED        0      0      0
  PCK1 WILD-TYPE     14     45     43
D14V12, multiclass

Clustering(15) Variable = ARID1A MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        2      0      0
  ARID1A WILD-TYPE     20     21      3
D15V1, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               44 
      TCGA-A3-3308       TCGA-A3-3311       TCGA-A3-3316       TCGA-A3-3317 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3319       TCGA-A3-3322       TCGA-A3-3323       TCGA-A3-3326 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3346       TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3362 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3365       TCGA-A3-3372       TCGA-A3-3378 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3380       TCGA-A3-3382       TCGA-A3-3383       TCGA-AK-3455 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-AK-3456       TCGA-AS-3778       TCGA-B2-3924       TCGA-B2-4098 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B2-4099       TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B8-4154       TCGA-B8-4620       TCGA-BP-4161       TCGA-BP-4162 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4164       TCGA-BP-4167       TCGA-CJ-4634 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CJ-4636       TCGA-CJ-4637       TCGA-CJ-4638       TCGA-CJ-4639 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4641       TCGA-CJ-4643       TCGA-CJ-4644 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ARID1A MUTATED        0      0      0      0      2      0      0
  ARID1A WILD-TYPE      4     10      3     10      8      8      1
D15V2, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               44 
      TCGA-A3-3308       TCGA-A3-3311       TCGA-A3-3316       TCGA-A3-3317 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3319       TCGA-A3-3322       TCGA-A3-3323       TCGA-A3-3326 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3346       TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3362 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3365       TCGA-A3-3372       TCGA-A3-3378 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A3-3380       TCGA-A3-3382       TCGA-A3-3383       TCGA-AK-3455 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-AK-3456       TCGA-AS-3778       TCGA-B2-3924       TCGA-B2-4098 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B2-4099       TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B8-4154       TCGA-B8-4620       TCGA-BP-4161       TCGA-BP-4162 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4164       TCGA-BP-4167       TCGA-CJ-4634 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CJ-4636       TCGA-CJ-4637       TCGA-CJ-4638       TCGA-CJ-4639 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4641       TCGA-CJ-4643       TCGA-CJ-4644 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        7      1      4
  ARID1A WILD-TYPE    183     94    126
D15V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7              183
  CLUS_2              1               94
  CLUS_3              4              126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        5      1      1
  ARID1A WILD-TYPE     91     52     93
D15V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               91
  CLUS_2              1               52
  CLUS_3              1               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 CLUS_5 CLUS_6
  ARID1A MUTATED        4      1      1      3      2      1
  ARID1A WILD-TYPE     89     55     66     61     66     37
D15V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               89
  CLUS_2              1               55
  CLUS_3              1               66
  CLUS_4              3               61
  CLUS_5              2               66
  CLUS_6              1               37
[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
  ARID1A MUTATED        3      6      3
  ARID1A WILD-TYPE    102    168    104
D15V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3              102
  CLUS_2              6              168
  CLUS_3              3              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      8      3
  ARID1A WILD-TYPE     67    169    167
D15V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               67
  CLUS_2              8              169
  CLUS_3              3              167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      8      3
  ARID1A WILD-TYPE    113    182    108
D15V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1              113
  CLUS_2              8              182
  CLUS_3              3              108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      8      3
  ARID1A WILD-TYPE     94    164    137
D15V9, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               94
  CLUS_2              8              164
  CLUS_3              3              137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        0      1     10      1
  ARID1A WILD-TYPE    112    100    149     34
D15V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0              112
  CLUS_2              1              100
  CLUS_3             10              149
  CLUS_4              1               34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARID1A MUTATED        1      0      2      0
  ARID1A WILD-TYPE     11     20     40     28
D15V11, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               11
  CLUS_2              0               20
  CLUS_3              2               40
  CLUS_4              0               28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ARID1A MUTATED        1      0      2
  ARID1A WILD-TYPE     13     45     41
D15V12, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               13
  CLUS_2              0               45
  CLUS_3              2               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = ATM MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        1      0      0
  ATM WILD-TYPE     21     21      3
D16V1, multiclass
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1            45 
   TCGA-A3-3308    TCGA-A3-3311    TCGA-A3-3316    TCGA-A3-3317    TCGA-A3-3319 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A3-3320    TCGA-A3-3322    TCGA-A3-3323    TCGA-A3-3326    TCGA-A3-3346 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A3-3347    TCGA-A3-3349    TCGA-A3-3362    TCGA-A3-3363    TCGA-A3-3365 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A3-3372    TCGA-A3-3378    TCGA-A3-3380    TCGA-A3-3382    TCGA-A3-3383 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-AK-3444    TCGA-AK-3455    TCGA-AK-3456    TCGA-AS-3778    TCGA-B2-3924 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B2-4098    TCGA-B2-4099    TCGA-B8-4143    TCGA-B8-4148    TCGA-B8-4151 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B8-4154    TCGA-B8-4620    TCGA-BP-4161    TCGA-BP-4162    TCGA-BP-4163 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4164    TCGA-BP-4167    TCGA-CJ-4634    TCGA-CJ-4636    TCGA-CJ-4637 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-4638    TCGA-CJ-4640    TCGA-CJ-4641    TCGA-CJ-4643    TCGA-CJ-4644 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ATM MUTATED        0      0      0      0      1      0      0
  ATM WILD-TYPE      4     10      3     10      9      8      1
D16V2, multiclass
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1            45 
   TCGA-A3-3308    TCGA-A3-3311    TCGA-A3-3316    TCGA-A3-3317    TCGA-A3-3319 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A3-3320    TCGA-A3-3322    TCGA-A3-3323    TCGA-A3-3326    TCGA-A3-3346 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A3-3347    TCGA-A3-3349    TCGA-A3-3362    TCGA-A3-3363    TCGA-A3-3365 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A3-3372    TCGA-A3-3378    TCGA-A3-3380    TCGA-A3-3382    TCGA-A3-3383 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-AK-3444    TCGA-AK-3455    TCGA-AK-3456    TCGA-AS-3778    TCGA-B2-3924 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B2-4098    TCGA-B2-4099    TCGA-B8-4143    TCGA-B8-4148    TCGA-B8-4151 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B8-4154    TCGA-B8-4620    TCGA-BP-4161    TCGA-BP-4162    TCGA-BP-4163 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4164    TCGA-BP-4167    TCGA-CJ-4634    TCGA-CJ-4636    TCGA-CJ-4637 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-4638    TCGA-CJ-4640    TCGA-CJ-4641    TCGA-CJ-4643    TCGA-CJ-4644 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        6      3      2
  ATM WILD-TYPE    184     92    128
D16V3, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           6           184
  CLUS_2           3            92
  CLUS_3           2           128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        5      1      2
  ATM WILD-TYPE     91     52     92
D16V4, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           5            91
  CLUS_2           1            52
  CLUS_3           2            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 CLUS_5 CLUS_6
  ATM MUTATED        3      1      0      3      2      1
  ATM WILD-TYPE     90     55     67     61     66     37
D16V5, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           3            90
  CLUS_2           1            55
  CLUS_3           0            67
  CLUS_4           3            61
  CLUS_5           2            66
  CLUS_6           1            37
[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
  ATM MUTATED        3      4      3
  ATM WILD-TYPE    102    170    104
D16V6, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           3           102
  CLUS_2           4           170
  CLUS_3           3           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        0      7      4
  ATM WILD-TYPE     68    170    166
D16V7, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           0            68
  CLUS_2           7           170
  CLUS_3           4           166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        0      9      2
  ATM WILD-TYPE    114    181    109
D16V8, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           0           114
  CLUS_2           9           181
  CLUS_3           2           109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        0      7      3
  ATM WILD-TYPE     95    165    137
D16V9, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           0            95
  CLUS_2           7           165
  CLUS_3           3           137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATM MUTATED        0      3      5      2
  ATM WILD-TYPE    112     98    154     33
D16V10, multiclass
        clus
vv       ATM MUTATED ATM WILD-TYPE
  CLUS_1           0           112
  CLUS_2           3            98
  CLUS_3           5           154
  CLUS_4           2            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATM MUTATED        0      0      0      1
  ATM WILD-TYPE     12     20     42     27
D16V11, multiclass
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1           101 
   TCGA-A3-3317    TCGA-A3-3358    TCGA-A3-3387    TCGA-AK-3458    TCGA-B0-4700 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-4706    TCGA-B0-4710    TCGA-B0-4712    TCGA-B0-4810    TCGA-B0-4811 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-4836    TCGA-B0-4837    TCGA-B0-4852    TCGA-B0-5080    TCGA-B0-5085 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-5088    TCGA-B0-5399    TCGA-B0-5691    TCGA-B0-5692    TCGA-B0-5693 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-5694    TCGA-B0-5695    TCGA-B0-5696    TCGA-B0-5699    TCGA-B0-5702 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-5705    TCGA-B0-5709    TCGA-B2-3924    TCGA-B2-5633    TCGA-B2-5635 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5377    TCGA-B8-4621    TCGA-B8-5545    TCGA-B8-5550    TCGA-B8-5551 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B8-5552    TCGA-B8-5553    TCGA-BP-4173    TCGA-BP-4340    TCGA-BP-4761 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4770    TCGA-BP-4787    TCGA-BP-4789    TCGA-BP-4790    TCGA-BP-4804 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4807    TCGA-BP-4961    TCGA-BP-4967    TCGA-BP-4968    TCGA-BP-4970 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4974    TCGA-BP-4976    TCGA-BP-4981    TCGA-BP-4982    TCGA-BP-4985 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4988    TCGA-BP-4989    TCGA-BP-4992    TCGA-BP-4995    TCGA-BP-4998 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-5001    TCGA-BP-5008    TCGA-BP-5009    TCGA-CJ-4870    TCGA-CJ-4875 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-4876    TCGA-CJ-4878    TCGA-CJ-4881    TCGA-CJ-4887    TCGA-CJ-4889 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-4890    TCGA-CJ-4895    TCGA-CJ-5671    TCGA-CJ-5675    TCGA-CJ-5676 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-5681    TCGA-CJ-5683    TCGA-CJ-6031    TCGA-CJ-6032    TCGA-CW-5585 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CW-5589    TCGA-CW-6087    TCGA-CZ-4854    TCGA-CZ-4857    TCGA-CZ-4858 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5453    TCGA-CZ-5454    TCGA-CZ-5455    TCGA-CZ-5457    TCGA-CZ-5459 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5462    TCGA-CZ-5463    TCGA-CZ-5466    TCGA-CZ-5467    TCGA-CZ-5469 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5470    TCGA-CZ-5989    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5569 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-EU-5904 
"ATM WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  ATM MUTATED        0      0      1
  ATM WILD-TYPE     14     45     42
D16V12, multiclass
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1           101 
   TCGA-A3-3317    TCGA-A3-3358    TCGA-A3-3387    TCGA-AK-3458    TCGA-B0-4700 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-4706    TCGA-B0-4710    TCGA-B0-4712    TCGA-B0-4810    TCGA-B0-4811 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-4836    TCGA-B0-4837    TCGA-B0-4852    TCGA-B0-5080    TCGA-B0-5085 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-5088    TCGA-B0-5399    TCGA-B0-5691    TCGA-B0-5692    TCGA-B0-5693 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-5694    TCGA-B0-5695    TCGA-B0-5696    TCGA-B0-5699    TCGA-B0-5702 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B0-5705    TCGA-B0-5709    TCGA-B2-3924    TCGA-B2-5633    TCGA-B2-5635 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5377    TCGA-B8-4621    TCGA-B8-5545    TCGA-B8-5550    TCGA-B8-5551 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B8-5552    TCGA-B8-5553    TCGA-BP-4173    TCGA-BP-4340    TCGA-BP-4761 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4770    TCGA-BP-4787    TCGA-BP-4789    TCGA-BP-4790    TCGA-BP-4804 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4807    TCGA-BP-4961    TCGA-BP-4967    TCGA-BP-4968    TCGA-BP-4970 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4974    TCGA-BP-4976    TCGA-BP-4981    TCGA-BP-4982    TCGA-BP-4985 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-4988    TCGA-BP-4989    TCGA-BP-4992    TCGA-BP-4995    TCGA-BP-4998 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-BP-5001    TCGA-BP-5008    TCGA-BP-5009    TCGA-CJ-4870    TCGA-CJ-4875 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-4876    TCGA-CJ-4878    TCGA-CJ-4881    TCGA-CJ-4887    TCGA-CJ-4889 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-4890    TCGA-CJ-4895    TCGA-CJ-5671    TCGA-CJ-5675    TCGA-CJ-5676 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-5681    TCGA-CJ-5683    TCGA-CJ-6031    TCGA-CJ-6032    TCGA-CW-5585 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CW-5589    TCGA-CW-6087    TCGA-CZ-4854    TCGA-CZ-4857    TCGA-CZ-4858 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5453    TCGA-CZ-5454    TCGA-CZ-5455    TCGA-CZ-5457    TCGA-CZ-5459 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5462    TCGA-CZ-5463    TCGA-CZ-5466    TCGA-CZ-5467    TCGA-CZ-5469 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5470    TCGA-CZ-5989    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5569 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-EU-5904 
"ATM WILD-TYPE" 

Clustering(17) Variable = DPCR1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        0      0      0
  DPCR1 WILD-TYPE     22     21      3
D17V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  DPCR1 MUTATED        0      0      0      0      0      0      0
  DPCR1 WILD-TYPE      4     10      3     10     10      8      1
D17V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        1      3      2
  DPCR1 WILD-TYPE    189     92    128
D17V3, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             1             189
  CLUS_2             3              92
  CLUS_3             2             128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        1      2      3
  DPCR1 WILD-TYPE     95     51     91
D17V4, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             1              95
  CLUS_2             2              51
  CLUS_3             3              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 CLUS_5 CLUS_6
  DPCR1 MUTATED        0      2      2      0      1      1
  DPCR1 WILD-TYPE     93     54     65     64     67     37
D17V5, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             0              93
  CLUS_2             2              54
  CLUS_3             2              65
  CLUS_4             0              64
  CLUS_5             1              67
  CLUS_6             1              37
[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
  DPCR1 MUTATED        1      3      2
  DPCR1 WILD-TYPE    104    171    105
D17V6, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             1             104
  CLUS_2             3             171
  CLUS_3             2             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        2      1      3
  DPCR1 WILD-TYPE     66    176    167
D17V7, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             2              66
  CLUS_2             1             176
  CLUS_3             3             167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        3      1      2
  DPCR1 WILD-TYPE    111    189    109
D17V8, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             3             111
  CLUS_2             1             189
  CLUS_3             2             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        2      2      2
  DPCR1 WILD-TYPE     93    170    138
D17V9, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             2              93
  CLUS_2             2             170
  CLUS_3             2             138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DPCR1 MUTATED        2      2      2      0
  DPCR1 WILD-TYPE    110     99    157     35
D17V10, multiclass
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  CLUS_1             2             110
  CLUS_2             2              99
  CLUS_3             2             157
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DPCR1 MUTATED        0      1      1      0
  DPCR1 WILD-TYPE     12     19     41     28
D17V11, multiclass
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              2             100 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5399 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693      TCGA-B0-5694 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699      TCGA-B0-5702 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924      TCGA-B2-5633 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857      TCGA-CZ-4858 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455      TCGA-CZ-5457 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463      TCGA-CZ-5466 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5989 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569      TCGA-EU-5904 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  DPCR1 MUTATED        0      2      0
  DPCR1 WILD-TYPE     14     43     43
D17V12, multiclass
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              2             100 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5399 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693      TCGA-B0-5694 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699      TCGA-B0-5702 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924      TCGA-B2-5633 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857      TCGA-CZ-4858 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455      TCGA-CZ-5457 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463      TCGA-CZ-5466 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5989 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569      TCGA-EU-5904 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 

Clustering(18) Variable = FGFR3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        0      0      0
  FGFR3 WILD-TYPE     22     21      3
D18V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  FGFR3 MUTATED        0      0      0      0      0      0      0
  FGFR3 WILD-TYPE      4     10      3     10     10      8      1
D18V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        2      0      2
  FGFR3 WILD-TYPE    188     95    128
D18V3, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             2             188
  CLUS_2             0              95
  CLUS_3             2             128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        1      1      2
  FGFR3 WILD-TYPE     95     52     92
D18V4, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             1              95
  CLUS_2             1              52
  CLUS_3             2              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 CLUS_5 CLUS_6
  FGFR3 MUTATED        1      0      0      1      1      0
  FGFR3 WILD-TYPE     92     56     67     63     67     38
D18V5, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             1              92
  CLUS_2             0              56
  CLUS_3             0              67
  CLUS_4             1              63
  CLUS_5             1              67
  CLUS_6             0              38
[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
  FGFR3 MUTATED        1      1      1
  FGFR3 WILD-TYPE    104    173    106
D18V6, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             1             104
  CLUS_2             1             173
  CLUS_3             1             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        1      2      1
  FGFR3 WILD-TYPE     67    175    169
D18V7, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             1              67
  CLUS_2             2             175
  CLUS_3             1             169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        0      2      2
  FGFR3 WILD-TYPE    114    188    109
D18V8, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             0             114
  CLUS_2             2             188
  CLUS_3             2             109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        1      1      2
  FGFR3 WILD-TYPE     94    171    138
D18V9, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             1              94
  CLUS_2             1             171
  CLUS_3             2             138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FGFR3 MUTATED        3      0      1      0
  FGFR3 WILD-TYPE    109    101    158     35
D18V10, multiclass
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  CLUS_1             3             109
  CLUS_2             0             101
  CLUS_3             1             158
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FGFR3 MUTATED        0      0      0      0
  FGFR3 WILD-TYPE     12     20     42     28
D18V11, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FGFR3 MUTATED        0      0      0
  FGFR3 WILD-TYPE     14     45     43
D18V12, multiclass

Clustering(19) Variable = PTCH1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        0      0      0
  PTCH1 WILD-TYPE     22     21      3
D19V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  PTCH1 MUTATED        0      0      0      0      0      0      0
  PTCH1 WILD-TYPE      4     10      3     10     10      8      1
D19V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        3      2      2
  PTCH1 WILD-TYPE    187     93    128
D19V3, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             3             187
  CLUS_2             2              93
  CLUS_3             2             128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        0      0      4
  PTCH1 WILD-TYPE     96     53     90
D19V4, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             0              96
  CLUS_2             0              53
  CLUS_3             4              90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  PTCH1 MUTATED        2      3      0      1      1      0
  PTCH1 WILD-TYPE     91     53     67     63     67     38
D19V5, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             2              91
  CLUS_2             3              53
  CLUS_3             0              67
  CLUS_4             1              63
  CLUS_5             1              67
  CLUS_6             0              38
[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
  PTCH1 MUTATED        2      1      4
  PTCH1 WILD-TYPE    103    173    103
D19V6, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             2             103
  CLUS_2             1             173
  CLUS_3             4             103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        1      4      2
  PTCH1 WILD-TYPE     67    173    168
D19V7, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             1              67
  CLUS_2             4             173
  CLUS_3             2             168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        3      4      0
  PTCH1 WILD-TYPE    111    186    111
D19V8, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             3             111
  CLUS_2             4             186
  CLUS_3             0             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        1      3      3
  PTCH1 WILD-TYPE     94    169    137
D19V9, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             1              94
  CLUS_2             3             169
  CLUS_3             3             137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTCH1 MUTATED        1      3      3      0
  PTCH1 WILD-TYPE    111     98    156     35
D19V10, multiclass
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  CLUS_1             1             111
  CLUS_2             3              98
  CLUS_3             3             156
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTCH1 MUTATED        0      0      0      0
  PTCH1 WILD-TYPE     12     20     42     28
D19V11, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PTCH1 MUTATED        0      0      0
  PTCH1 WILD-TYPE     14     45     43
D19V12, multiclass

Clustering(20) Variable = RBMX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        1      0      0
  RBMX WILD-TYPE     21     21      3
D20V1, multiclass
[1] "Remove cluster labels:" "RBMX MUTATED"          
clus
  RBMX MUTATED RBMX WILD-TYPE 
             1             45 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3347     TCGA-A3-3349 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3362     TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3372 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3378     TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3383 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-AK-3444     TCGA-AK-3455     TCGA-AK-3456     TCGA-B2-3924 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B2-4098     TCGA-B2-4099     TCGA-B8-4143     TCGA-B8-4148 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4644 
"RBMX WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  RBMX MUTATED        0      0      0      0      0      1      0
  RBMX WILD-TYPE      4     10      3     10     10      7      1
D20V2, multiclass
[1] "Remove cluster labels:" "RBMX MUTATED"          
clus
  RBMX MUTATED RBMX WILD-TYPE 
             1             45 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3347     TCGA-A3-3349 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3362     TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3372 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-A3-3378     TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3383 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-AK-3444     TCGA-AK-3455     TCGA-AK-3456     TCGA-B2-3924 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B2-4098     TCGA-B2-4099     TCGA-B8-4143     TCGA-B8-4148 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4644 
"RBMX WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        2      0      2
  RBMX WILD-TYPE    188     95    128
D20V3, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            2            188
  CLUS_2            0             95
  CLUS_3            2            128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        1      0      2
  RBMX WILD-TYPE     95     53     92
D20V4, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1             95
  CLUS_2            0             53
  CLUS_3            2             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 CLUS_5 CLUS_6
  RBMX MUTATED        0      2      0      0      1      0
  RBMX WILD-TYPE     93     54     67     64     67     38
D20V5, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0             93
  CLUS_2            2             54
  CLUS_3            0             67
  CLUS_4            0             64
  CLUS_5            1             67
  CLUS_6            0             38
[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
  RBMX MUTATED        0      1      2
  RBMX WILD-TYPE    105    173    105
D20V6, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0            105
  CLUS_2            1            173
  CLUS_3            2            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        0      1      3
  RBMX WILD-TYPE     68    176    167
D20V7, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            0             68
  CLUS_2            1            176
  CLUS_3            3            167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        1      1      2
  RBMX WILD-TYPE    113    189    109
D20V8, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1            113
  CLUS_2            1            189
  CLUS_3            2            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        1      0      2
  RBMX WILD-TYPE     94    172    138
D20V9, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1             94
  CLUS_2            0            172
  CLUS_3            2            138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RBMX MUTATED        1      1      0      1
  RBMX WILD-TYPE    111    100    159     34
D20V10, multiclass
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  CLUS_1            1            111
  CLUS_2            1            100
  CLUS_3            0            159
  CLUS_4            1             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RBMX MUTATED        0      0      0      1
  RBMX WILD-TYPE     12     20     42     27
D20V11, multiclass
[1] "Remove cluster labels:" "RBMX MUTATED"          
clus
  RBMX MUTATED RBMX WILD-TYPE 
             1            101 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-A3-3387     TCGA-AK-3458 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-4700     TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4810 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4836     TCGA-B0-4837     TCGA-B0-4852 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5080     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5399 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5699     TCGA-B0-5702 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5709     TCGA-B2-3924     TCGA-B2-5633 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4621     TCGA-B8-5545 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5552     TCGA-B8-5553 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4340     TCGA-BP-4761     TCGA-BP-4770 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4787     TCGA-BP-4789     TCGA-BP-4790     TCGA-BP-4804 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4807     TCGA-BP-4961     TCGA-BP-4967     TCGA-BP-4968 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4974     TCGA-BP-4976     TCGA-BP-4981 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4988     TCGA-BP-4989 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4992     TCGA-BP-4995     TCGA-BP-4998     TCGA-BP-5001 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4870     TCGA-CJ-4875 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4878     TCGA-CJ-4881     TCGA-CJ-4887 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4889     TCGA-CJ-4890     TCGA-CJ-4895     TCGA-CJ-5671 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-5675     TCGA-CJ-5676     TCGA-CJ-5681     TCGA-CJ-5683 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-5686     TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CW-5585 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CW-5589     TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4857 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-4858     TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5455 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5459     TCGA-CZ-5462     TCGA-CZ-5463 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-5466     TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-5989     TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5569 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-EU-5904 
"RBMX WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RBMX MUTATED        0      1      0
  RBMX WILD-TYPE     14     44     43
D20V12, multiclass
[1] "Remove cluster labels:" "RBMX MUTATED"          
clus
  RBMX MUTATED RBMX WILD-TYPE 
             1            101 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-A3-3387     TCGA-AK-3458 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-4700     TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4810 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4836     TCGA-B0-4837     TCGA-B0-4852 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5080     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5399 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5699     TCGA-B0-5702 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5709     TCGA-B2-3924     TCGA-B2-5633 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4621     TCGA-B8-5545 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5552     TCGA-B8-5553 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4340     TCGA-BP-4761     TCGA-BP-4770 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4787     TCGA-BP-4789     TCGA-BP-4790     TCGA-BP-4804 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4807     TCGA-BP-4961     TCGA-BP-4967     TCGA-BP-4968 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4974     TCGA-BP-4976     TCGA-BP-4981 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4988     TCGA-BP-4989 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-4992     TCGA-BP-4995     TCGA-BP-4998     TCGA-BP-5001 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4870     TCGA-CJ-4875 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4878     TCGA-CJ-4881     TCGA-CJ-4887 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-4889     TCGA-CJ-4890     TCGA-CJ-4895     TCGA-CJ-5671 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-5675     TCGA-CJ-5676     TCGA-CJ-5681     TCGA-CJ-5683 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CJ-5686     TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CW-5585 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CW-5589     TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4857 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-4858     TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5455 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5459     TCGA-CZ-5462     TCGA-CZ-5463 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-5466     TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-CZ-5989     TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5569 
"RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" "RBMX WILD-TYPE" 
    TCGA-EU-5904 
"RBMX WILD-TYPE" 

Clustering(21) Variable = ARAP3 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        0      1      0
  ARAP3 WILD-TYPE     22     20      3
D21V1, multiclass
[1] "Remove cluster labels:" "ARAP3 MUTATED"         
clus
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1              45 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3319      TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3326 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3346      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3362 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3365      TCGA-A3-3372      TCGA-A3-3378 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3380      TCGA-A3-3382      TCGA-A3-3383      TCGA-AK-3444 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-AK-3455      TCGA-AK-3456      TCGA-AS-3778      TCGA-B2-3924 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B2-4098      TCGA-B2-4099      TCGA-B8-4143      TCGA-B8-4148 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4620      TCGA-BP-4161 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4167 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4634      TCGA-CJ-4636      TCGA-CJ-4637      TCGA-CJ-4638 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4641      TCGA-CJ-4643 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4644 
"ARAP3 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  ARAP3 MUTATED        0      1      0      0      0      0      0
  ARAP3 WILD-TYPE      4      9      3     10     10      8      1
D21V2, multiclass
[1] "Remove cluster labels:" "ARAP3 MUTATED"         
clus
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1              45 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3319      TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3326 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3346      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3362 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3365      TCGA-A3-3372      TCGA-A3-3378 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3380      TCGA-A3-3382      TCGA-A3-3383      TCGA-AK-3444 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-AK-3455      TCGA-AK-3456      TCGA-AS-3778      TCGA-B2-3924 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B2-4098      TCGA-B2-4099      TCGA-B8-4143      TCGA-B8-4148 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4620      TCGA-BP-4161 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4167 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4634      TCGA-CJ-4636      TCGA-CJ-4637      TCGA-CJ-4638 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4641      TCGA-CJ-4643 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4644 
"ARAP3 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        2      1      0
  ARAP3 WILD-TYPE    188     94    130
D21V3, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             2             188
  CLUS_2             1              94
  CLUS_3             0             130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        0      1      0
  ARAP3 WILD-TYPE     96     52     94
D21V4, multiclass
[1] "Remove cluster labels:" "ARAP3 MUTATED"         
clus
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1             242 
     TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3367      TCGA-A3-3370 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-A3-3373      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3428      TCGA-AK-3431      TCGA-AK-3434 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3450      TCGA-AK-3454      TCGA-AK-3458 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-AK-3460      TCGA-AK-3461      TCGA-B0-4690      TCGA-B0-4691 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4693      TCGA-B0-4694      TCGA-B0-4697      TCGA-B0-4700 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4703      TCGA-B0-4706      TCGA-B0-4707      TCGA-B0-4710 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4712      TCGA-B0-4713      TCGA-B0-4714      TCGA-B0-4718 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4813      TCGA-B0-4814 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4815      TCGA-B0-4816      TCGA-B0-4817      TCGA-B0-4818 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4822      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4828      TCGA-B0-4841      TCGA-B0-4842      TCGA-B0-4843 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4844      TCGA-B0-4845      TCGA-B0-4846      TCGA-B0-4847 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4848      TCGA-B0-4849      TCGA-B0-4852      TCGA-B0-4945 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5080      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5099      TCGA-B0-5100 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5102      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5402 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693      TCGA-B0-5694 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5698 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5699      TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5709 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5710      TCGA-B0-5711      TCGA-B0-5713      TCGA-B0-5812 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B2-3924      TCGA-B2-4101      TCGA-B2-5633      TCGA-B2-5635 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B2-5641      TCGA-B4-5377      TCGA-B8-4146      TCGA-B8-4153 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5552      TCGA-B8-5553      TCGA-BP-4770      TCGA-BP-4782 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4801      TCGA-BP-4993      TCGA-BP-5010      TCGA-BP-5168 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5169      TCGA-BP-5170      TCGA-BP-5173      TCGA-BP-5174 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5175      TCGA-BP-5176      TCGA-BP-5177      TCGA-BP-5178 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5180      TCGA-BP-5182      TCGA-BP-5183      TCGA-BP-5184 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5185      TCGA-BP-5186      TCGA-BP-5187      TCGA-BP-5189 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5190      TCGA-BP-5191      TCGA-BP-5192      TCGA-BP-5194 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5195      TCGA-BP-5196      TCGA-BP-5198      TCGA-BP-5199 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5200      TCGA-BP-5201      TCGA-BP-5202      TCGA-CJ-4882 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4897      TCGA-CJ-4901      TCGA-CJ-4902      TCGA-CJ-4903 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-4905      TCGA-CJ-4907      TCGA-CJ-4908 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4912      TCGA-CJ-4913      TCGA-CJ-4916      TCGA-CJ-4918 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4920      TCGA-CJ-4923      TCGA-CJ-5671      TCGA-CJ-5672 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5677      TCGA-CJ-5678 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5679      TCGA-CJ-5680      TCGA-CJ-5681      TCGA-CJ-5682 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5683      TCGA-CJ-5684      TCGA-CJ-5686      TCGA-CJ-6027 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-6028      TCGA-CJ-6030      TCGA-CJ-6031      TCGA-CJ-6032 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-6033      TCGA-CW-5580      TCGA-CW-5581      TCGA-CW-5583 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5588      TCGA-CW-5589      TCGA-CW-5591 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CW-6087      TCGA-CW-6090      TCGA-CW-6093      TCGA-CZ-4853 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-4865 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-4866      TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5453 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5454      TCGA-CZ-5455      TCGA-CZ-5456      TCGA-CZ-5457 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5458      TCGA-CZ-5459      TCGA-CZ-5460      TCGA-CZ-5461 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5462      TCGA-CZ-5463      TCGA-CZ-5465      TCGA-CZ-5466 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5468      TCGA-CZ-5469      TCGA-CZ-5470 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-CZ-5984      TCGA-CZ-5985      TCGA-CZ-5986 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5987      TCGA-CZ-5988      TCGA-CZ-5989      TCGA-DV-5565 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-EU-5906      TCGA-EU-5907 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  ARAP3 MUTATED        1      0      1      0      1      0
  ARAP3 WILD-TYPE     92     56     66     64     67     38
D21V5, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             1              92
  CLUS_2             0              56
  CLUS_3             1              66
  CLUS_4             0              64
  CLUS_5             1              67
  CLUS_6             0              38
[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
  ARAP3 MUTATED        1      1      1
  ARAP3 WILD-TYPE    104    173    106
D21V6, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             1             104
  CLUS_2             1             173
  CLUS_3             1             106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        0      1      2
  ARAP3 WILD-TYPE     68    176    168
D21V7, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             0              68
  CLUS_2             1             176
  CLUS_3             2             168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        1      1      1
  ARAP3 WILD-TYPE    113    189    110
D21V8, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             1             113
  CLUS_2             1             189
  CLUS_3             1             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        0      2      1
  ARAP3 WILD-TYPE     95    170    139
D21V9, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             0              95
  CLUS_2             2             170
  CLUS_3             1             139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARAP3 MUTATED        1      0      2      0
  ARAP3 WILD-TYPE    111    101    157     35
D21V10, multiclass
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  CLUS_1             1             111
  CLUS_2             0             101
  CLUS_3             2             157
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ARAP3 MUTATED        1      0      0      0
  ARAP3 WILD-TYPE     11     20     42     28
D21V11, multiclass
[1] "Remove cluster labels:" "ARAP3 MUTATED"         
clus
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1             101 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4804      TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4981      TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4989      TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5001      TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4875 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5466      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5989      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-EU-5904 
"ARAP3 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  ARAP3 MUTATED        1      0      0
  ARAP3 WILD-TYPE     13     45     43
D21V12, multiclass
[1] "Remove cluster labels:" "ARAP3 MUTATED"         
clus
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1             101 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4804      TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4981      TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-4989      TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-BP-5001      TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4875 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5466      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-CZ-5989      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569 
"ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" "ARAP3 WILD-TYPE" 
     TCGA-EU-5904 
"ARAP3 WILD-TYPE" 

Clustering(22) Variable = GPR172B MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        0      0      0
  GPR172B WILD-TYPE     22     21      3
D22V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  GPR172B MUTATED        0      0      0      0      0      0      0
  GPR172B WILD-TYPE      4     10      3     10     10      8      1
D22V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        2      1      1
  GPR172B WILD-TYPE    188     94    129
D22V3, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               2               188
  CLUS_2               1                94
  CLUS_3               1               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        0      1      0
  GPR172B WILD-TYPE     96     52     94
D22V4, multiclass
[1] "Remove cluster labels:" "GPR172B MUTATED"       
clus
  GPR172B MUTATED GPR172B WILD-TYPE 
                1               242 
       TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3367        TCGA-A3-3370 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-A3-3373        TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-AK-3425        TCGA-AK-3428        TCGA-AK-3431        TCGA-AK-3434 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-AK-3445        TCGA-AK-3450        TCGA-AK-3454        TCGA-AK-3458 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-AK-3460        TCGA-AK-3461        TCGA-B0-4690        TCGA-B0-4691 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4693        TCGA-B0-4694        TCGA-B0-4697        TCGA-B0-4700 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4703        TCGA-B0-4706        TCGA-B0-4707        TCGA-B0-4710 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4712        TCGA-B0-4713        TCGA-B0-4714        TCGA-B0-4718 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4813        TCGA-B0-4814 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4818 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4819        TCGA-B0-4822        TCGA-B0-4823        TCGA-B0-4824 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4827        TCGA-B0-4828        TCGA-B0-4841        TCGA-B0-4842 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4843        TCGA-B0-4844        TCGA-B0-4845        TCGA-B0-4846 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4847        TCGA-B0-4848        TCGA-B0-4849        TCGA-B0-4852 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4945        TCGA-B0-5080        TCGA-B0-5092        TCGA-B0-5094 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5095        TCGA-B0-5096        TCGA-B0-5097        TCGA-B0-5099 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5100        TCGA-B0-5102        TCGA-B0-5104        TCGA-B0-5106 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5107        TCGA-B0-5108        TCGA-B0-5109        TCGA-B0-5110 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5113        TCGA-B0-5115        TCGA-B0-5116        TCGA-B0-5119 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5120        TCGA-B0-5121        TCGA-B0-5399        TCGA-B0-5400 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5402        TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5697 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5707 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5709        TCGA-B0-5710        TCGA-B0-5711        TCGA-B0-5713 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5812        TCGA-B2-3924        TCGA-B2-4101        TCGA-B2-5633 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B2-5635        TCGA-B2-5641        TCGA-B4-5377        TCGA-B8-4146 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-4153        TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5159        TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5545        TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5551        TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4770 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4801        TCGA-BP-4993        TCGA-BP-5010        TCGA-BP-5168 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5169        TCGA-BP-5170        TCGA-BP-5173        TCGA-BP-5174 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5175        TCGA-BP-5176        TCGA-BP-5177        TCGA-BP-5178 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5180        TCGA-BP-5182        TCGA-BP-5183        TCGA-BP-5184 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5185        TCGA-BP-5186        TCGA-BP-5187        TCGA-BP-5189 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5190        TCGA-BP-5191        TCGA-BP-5192        TCGA-BP-5194 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5195        TCGA-BP-5196        TCGA-BP-5198        TCGA-BP-5199 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5200        TCGA-BP-5201        TCGA-BP-5202        TCGA-CJ-4882 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4897        TCGA-CJ-4901        TCGA-CJ-4902        TCGA-CJ-4903 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4904        TCGA-CJ-4905        TCGA-CJ-4907        TCGA-CJ-4908 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4912        TCGA-CJ-4913        TCGA-CJ-4916        TCGA-CJ-4918 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4920        TCGA-CJ-4923        TCGA-CJ-5671        TCGA-CJ-5672 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5677        TCGA-CJ-5678 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5679        TCGA-CJ-5680        TCGA-CJ-5681        TCGA-CJ-5682 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5683        TCGA-CJ-5684        TCGA-CJ-5686        TCGA-CJ-6027 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CW-5585        TCGA-CW-5588        TCGA-CW-5589        TCGA-CW-5591 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CW-6087        TCGA-CW-6090        TCGA-CW-6093        TCGA-CZ-4853 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-4865 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-4866        TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5454        TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5462        TCGA-CZ-5463        TCGA-CZ-5465        TCGA-CZ-5466 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5469        TCGA-CZ-5470 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5982        TCGA-CZ-5984        TCGA-CZ-5985        TCGA-CZ-5986 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5987        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-DV-5565 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-EU-5906        TCGA-EU-5907 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  GPR172B MUTATED        0      1      0      2      0      0
  GPR172B WILD-TYPE     93     55     67     62     68     38
D22V5, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               0                93
  CLUS_2               1                55
  CLUS_3               0                67
  CLUS_4               2                62
  CLUS_5               0                68
  CLUS_6               0                38
[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
  GPR172B MUTATED        0      2      1
  GPR172B WILD-TYPE    105    172    106
D22V6, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               0               105
  CLUS_2               2               172
  CLUS_3               1               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        0      3      1
  GPR172B WILD-TYPE     68    174    169
D22V7, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               0                68
  CLUS_2               3               174
  CLUS_3               1               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        1      2      1
  GPR172B WILD-TYPE    113    188    110
D22V8, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               1               113
  CLUS_2               2               188
  CLUS_3               1               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        0      1      2
  GPR172B WILD-TYPE     95    171    138
D22V9, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               0                95
  CLUS_2               1               171
  CLUS_3               2               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPR172B MUTATED        1      1      1      0
  GPR172B WILD-TYPE    111    100    158     35
D22V10, multiclass
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  CLUS_1               1               111
  CLUS_2               1               100
  CLUS_3               1               158
  CLUS_4               0                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  GPR172B MUTATED        0      0      0      1
  GPR172B WILD-TYPE     12     20     42     27
D22V11, multiclass
[1] "Remove cluster labels:" "GPR172B MUTATED"       
clus
  GPR172B MUTATED GPR172B WILD-TYPE 
                1               101 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4700        TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4836        TCGA-B0-4837 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5080        TCGA-B0-5085        TCGA-B0-5088 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5699 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5705        TCGA-B0-5709        TCGA-B2-3924 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B2-5633        TCGA-B2-5635        TCGA-B4-5377        TCGA-B8-4621 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5545        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4340        TCGA-BP-4770 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4804 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4807        TCGA-BP-4961        TCGA-BP-4967        TCGA-BP-4968 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4970        TCGA-BP-4974        TCGA-BP-4976        TCGA-BP-4981 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4988        TCGA-BP-4989 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4992        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5001 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4870        TCGA-CJ-4875 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4895        TCGA-CJ-5671 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5681        TCGA-CJ-5683 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CW-5585 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4857 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5459        TCGA-CZ-5462        TCGA-CZ-5463 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5470 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5569 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-EU-5904 
"GPR172B WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  GPR172B MUTATED        0      1      0
  GPR172B WILD-TYPE     14     44     43
D22V12, multiclass
[1] "Remove cluster labels:" "GPR172B MUTATED"       
clus
  GPR172B MUTATED GPR172B WILD-TYPE 
                1               101 
       TCGA-A3-3317        TCGA-A3-3358        TCGA-A3-3387        TCGA-AK-3458 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4700        TCGA-B0-4706        TCGA-B0-4710        TCGA-B0-4712 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4836        TCGA-B0-4837 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-5080        TCGA-B0-5085        TCGA-B0-5088 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5699 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5705        TCGA-B0-5709        TCGA-B2-3924 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B2-5633        TCGA-B2-5635        TCGA-B4-5377        TCGA-B8-4621 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5545        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5552 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4173        TCGA-BP-4340        TCGA-BP-4770 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4787        TCGA-BP-4789        TCGA-BP-4790        TCGA-BP-4804 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4807        TCGA-BP-4961        TCGA-BP-4967        TCGA-BP-4968 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4970        TCGA-BP-4974        TCGA-BP-4976        TCGA-BP-4981 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4982        TCGA-BP-4985        TCGA-BP-4988        TCGA-BP-4989 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-4992        TCGA-BP-4995        TCGA-BP-4998        TCGA-BP-5001 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-BP-5008        TCGA-BP-5009        TCGA-CJ-4870        TCGA-CJ-4875 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4878        TCGA-CJ-4881        TCGA-CJ-4887 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-4889        TCGA-CJ-4890        TCGA-CJ-4895        TCGA-CJ-5671 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5675        TCGA-CJ-5676        TCGA-CJ-5681        TCGA-CJ-5683 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CW-5585 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CW-5589        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4857 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-5453        TCGA-CZ-5454        TCGA-CZ-5455 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5459        TCGA-CZ-5462        TCGA-CZ-5463 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5470 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-CZ-5989        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5569 
"GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" "GPR172B WILD-TYPE" 
       TCGA-EU-5904 
"GPR172B WILD-TYPE" 

Clustering(23) Variable = EGFR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        0      0      0
  EGFR WILD-TYPE     22     21      3
D23V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  EGFR MUTATED        0      0      0      0      0      0      0
  EGFR WILD-TYPE      4     10      3     10     10      8      1
D23V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        4      2      1
  EGFR WILD-TYPE    186     93    129
D23V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            4            186
  CLUS_2            2             93
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        2      0      2
  EGFR WILD-TYPE     94     53     92
D23V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            2             94
  CLUS_2            0             53
  CLUS_3            2             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 CLUS_5 CLUS_6
  EGFR MUTATED        2      2      0      1      1      1
  EGFR WILD-TYPE     91     54     67     63     67     37
D23V5, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            2             91
  CLUS_2            2             54
  CLUS_3            0             67
  CLUS_4            1             63
  CLUS_5            1             67
  CLUS_6            1             37
[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
  EGFR MUTATED        3      2      2
  EGFR WILD-TYPE    102    172    105
D23V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            3            102
  CLUS_2            2            172
  CLUS_3            2            105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        0      3      4
  EGFR WILD-TYPE     68    174    166
D23V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             68
  CLUS_2            3            174
  CLUS_3            4            166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        0      4      3
  EGFR WILD-TYPE    114    186    108
D23V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0            114
  CLUS_2            4            186
  CLUS_3            3            108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        1      3      2
  EGFR WILD-TYPE     94    169    138
D23V9, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            1             94
  CLUS_2            3            169
  CLUS_3            2            138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED        0      1      3      2
  EGFR WILD-TYPE    112    100    156     33
D23V10, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0            112
  CLUS_2            1            100
  CLUS_3            3            156
  CLUS_4            2             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED        0      0      0      0
  EGFR WILD-TYPE     12     20     42     28
D23V11, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        0      0      0
  EGFR WILD-TYPE     14     45     43
D23V12, multiclass

Clustering(24) Variable = IL1RAP MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        0      0      0
  IL1RAP WILD-TYPE     22     21      3
D24V1, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  IL1RAP MUTATED        0      0      0      0      0      0      0
  IL1RAP WILD-TYPE      4     10      3     10     10      8      1
D24V2, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        3      0      1
  IL1RAP WILD-TYPE    187     95    129
D24V3, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              3              187
  CLUS_2              0               95
  CLUS_3              1              129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        1      0      2
  IL1RAP WILD-TYPE     95     53     92
D24V4, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              1               95
  CLUS_2              0               53
  CLUS_3              2               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 CLUS_5 CLUS_6
  IL1RAP MUTATED        3      1      0      0      0      0
  IL1RAP WILD-TYPE     90     55     67     64     68     38
D24V5, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              3               90
  CLUS_2              1               55
  CLUS_3              0               67
  CLUS_4              0               64
  CLUS_5              0               68
  CLUS_6              0               38
[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
  IL1RAP MUTATED        2      0      2
  IL1RAP WILD-TYPE    103    174    105
D24V6, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              2              103
  CLUS_2              0              174
  CLUS_3              2              105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        1      2      1
  IL1RAP WILD-TYPE     67    175    169
D24V7, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              1               67
  CLUS_2              2              175
  CLUS_3              1              169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        0      3      1
  IL1RAP WILD-TYPE    114    187    110
D24V8, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              0              114
  CLUS_2              3              187
  CLUS_3              1              110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        0      3      1
  IL1RAP WILD-TYPE     95    169    139
D24V9, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              0               95
  CLUS_2              3              169
  CLUS_3              1              139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IL1RAP MUTATED        1      0      3      0
  IL1RAP WILD-TYPE    111    101    156     35
D24V10, multiclass
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  CLUS_1              1              111
  CLUS_2              0              101
  CLUS_3              3              156
  CLUS_4              0               35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IL1RAP MUTATED        0      0      0      1
  IL1RAP WILD-TYPE     12     20     42     27
D24V11, multiclass
[1] "Remove cluster labels:" "IL1RAP MUTATED"        
clus
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               1              101 
      TCGA-A3-3317       TCGA-A3-3358       TCGA-A3-3387       TCGA-AK-3458 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-4700       TCGA-B0-4706       TCGA-B0-4710       TCGA-B0-4712 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4836       TCGA-B0-4837 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-4852       TCGA-B0-5080       TCGA-B0-5085       TCGA-B0-5088 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-5399       TCGA-B0-5691       TCGA-B0-5692       TCGA-B0-5693 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696       TCGA-B0-5699 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5705       TCGA-B0-5709       TCGA-B2-3924 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5635       TCGA-B4-5377       TCGA-B8-4621 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B8-5545       TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5552 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4173       TCGA-BP-4340       TCGA-BP-4761 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4770       TCGA-BP-4787       TCGA-BP-4789       TCGA-BP-4790 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4804       TCGA-BP-4807       TCGA-BP-4961       TCGA-BP-4967 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4974       TCGA-BP-4976 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4981       TCGA-BP-4982       TCGA-BP-4988       TCGA-BP-4989 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4992       TCGA-BP-4995       TCGA-BP-4998       TCGA-BP-5001 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-5008       TCGA-BP-5009       TCGA-CJ-4870       TCGA-CJ-4875 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4878       TCGA-CJ-4881       TCGA-CJ-4887 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-4889       TCGA-CJ-4890       TCGA-CJ-4895       TCGA-CJ-5671 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-5675       TCGA-CJ-5676       TCGA-CJ-5681       TCGA-CJ-5683 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-5686       TCGA-CJ-6031       TCGA-CJ-6032       TCGA-CW-5585 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CW-5589       TCGA-CW-6087       TCGA-CZ-4854       TCGA-CZ-4857 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-5453       TCGA-CZ-5454       TCGA-CZ-5455 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5459       TCGA-CZ-5462       TCGA-CZ-5463 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-5466       TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-5989       TCGA-DV-5565       TCGA-DV-5566       TCGA-DV-5569 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-EU-5904 
"IL1RAP WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  IL1RAP MUTATED        0      1      0
  IL1RAP WILD-TYPE     14     44     43
D24V12, multiclass
[1] "Remove cluster labels:" "IL1RAP MUTATED"        
clus
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               1              101 
      TCGA-A3-3317       TCGA-A3-3358       TCGA-A3-3387       TCGA-AK-3458 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-4700       TCGA-B0-4706       TCGA-B0-4710       TCGA-B0-4712 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4836       TCGA-B0-4837 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-4852       TCGA-B0-5080       TCGA-B0-5085       TCGA-B0-5088 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-5399       TCGA-B0-5691       TCGA-B0-5692       TCGA-B0-5693 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696       TCGA-B0-5699 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5705       TCGA-B0-5709       TCGA-B2-3924 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5635       TCGA-B4-5377       TCGA-B8-4621 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B8-5545       TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5552 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4173       TCGA-BP-4340       TCGA-BP-4761 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4770       TCGA-BP-4787       TCGA-BP-4789       TCGA-BP-4790 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4804       TCGA-BP-4807       TCGA-BP-4961       TCGA-BP-4967 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4974       TCGA-BP-4976 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4981       TCGA-BP-4982       TCGA-BP-4988       TCGA-BP-4989 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-4992       TCGA-BP-4995       TCGA-BP-4998       TCGA-BP-5001 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-BP-5008       TCGA-BP-5009       TCGA-CJ-4870       TCGA-CJ-4875 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4878       TCGA-CJ-4881       TCGA-CJ-4887 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-4889       TCGA-CJ-4890       TCGA-CJ-4895       TCGA-CJ-5671 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-5675       TCGA-CJ-5676       TCGA-CJ-5681       TCGA-CJ-5683 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CJ-5686       TCGA-CJ-6031       TCGA-CJ-6032       TCGA-CW-5585 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CW-5589       TCGA-CW-6087       TCGA-CZ-4854       TCGA-CZ-4857 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-5453       TCGA-CZ-5454       TCGA-CZ-5455 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5459       TCGA-CZ-5462       TCGA-CZ-5463 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-5466       TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-CZ-5989       TCGA-DV-5565       TCGA-DV-5566       TCGA-DV-5569 
"IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" "IL1RAP WILD-TYPE" 
      TCGA-EU-5904 
"IL1RAP WILD-TYPE" 

Clustering(25) Variable = BCL6 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        0      0      0
  BCL6 WILD-TYPE     22     21      3
D25V1, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  BCL6 MUTATED        0      0      0      0      0      0      0
  BCL6 WILD-TYPE      4     10      3     10     10      8      1
D25V2, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        4      0      1
  BCL6 WILD-TYPE    186     95    129
D25V3, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            4            186
  CLUS_2            0             95
  CLUS_3            1            129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        1      0      2
  BCL6 WILD-TYPE     95     53     92
D25V4, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            1             95
  CLUS_2            0             53
  CLUS_3            2             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 CLUS_5 CLUS_6
  BCL6 MUTATED        1      1      2      0      1      0
  BCL6 WILD-TYPE     92     55     65     64     67     38
D25V5, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            1             92
  CLUS_2            1             55
  CLUS_3            2             65
  CLUS_4            0             64
  CLUS_5            1             67
  CLUS_6            0             38
[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
  BCL6 MUTATED        2      2      1
  BCL6 WILD-TYPE    103    172    106
D25V6, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            2            103
  CLUS_2            2            172
  CLUS_3            1            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        1      2      2
  BCL6 WILD-TYPE     67    175    168
D25V7, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            1             67
  CLUS_2            2            175
  CLUS_3            2            168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        0      3      2
  BCL6 WILD-TYPE    114    187    109
D25V8, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            0            114
  CLUS_2            3            187
  CLUS_3            2            109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        2      2      1
  BCL6 WILD-TYPE     93    170    139
D25V9, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            2             93
  CLUS_2            2            170
  CLUS_3            1            139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BCL6 MUTATED        1      2      1      1
  BCL6 WILD-TYPE    111     99    158     34
D25V10, multiclass
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  CLUS_1            1            111
  CLUS_2            2             99
  CLUS_3            1            158
  CLUS_4            1             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BCL6 MUTATED        0      1      0      1
  BCL6 WILD-TYPE     12     19     42     27
D25V11, multiclass
[1] "Remove cluster labels:" "BCL6 MUTATED"          
clus
  BCL6 MUTATED BCL6 WILD-TYPE 
             2            100 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-AK-3458     TCGA-B0-4700 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4712     TCGA-B0-4810 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4836     TCGA-B0-4837     TCGA-B0-4852 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5080     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5399 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5699     TCGA-B0-5702 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5709     TCGA-B2-3924     TCGA-B2-5633 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4621     TCGA-B8-5545 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5552     TCGA-B8-5553 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4340     TCGA-BP-4761     TCGA-BP-4770 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4787     TCGA-BP-4789     TCGA-BP-4790     TCGA-BP-4804 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4807     TCGA-BP-4961     TCGA-BP-4967     TCGA-BP-4968 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4974     TCGA-BP-4976     TCGA-BP-4981 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4988     TCGA-BP-4989 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4992     TCGA-BP-4995     TCGA-BP-4998     TCGA-BP-5001 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4870     TCGA-CJ-4875 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4878     TCGA-CJ-4881     TCGA-CJ-4887 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-4889     TCGA-CJ-4890     TCGA-CJ-5671     TCGA-CJ-5675 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-5676     TCGA-CJ-5681     TCGA-CJ-5683     TCGA-CJ-5686 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CW-5585     TCGA-CW-5589 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4857     TCGA-CZ-4858 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5455     TCGA-CZ-5457 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CZ-5459     TCGA-CZ-5462     TCGA-CZ-5463     TCGA-CZ-5466 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5989 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5569     TCGA-EU-5904 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BCL6 MUTATED        0      2      0
  BCL6 WILD-TYPE     14     43     43
D25V12, multiclass
[1] "Remove cluster labels:" "BCL6 MUTATED"          
clus
  BCL6 MUTATED BCL6 WILD-TYPE 
             2            100 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-AK-3458     TCGA-B0-4700 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4712     TCGA-B0-4810 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4836     TCGA-B0-4837     TCGA-B0-4852 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5080     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5399 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5699     TCGA-B0-5702 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5709     TCGA-B2-3924     TCGA-B2-5633 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4621     TCGA-B8-5545 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5552     TCGA-B8-5553 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4340     TCGA-BP-4761     TCGA-BP-4770 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4787     TCGA-BP-4789     TCGA-BP-4790     TCGA-BP-4804 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4807     TCGA-BP-4961     TCGA-BP-4967     TCGA-BP-4968 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4974     TCGA-BP-4976     TCGA-BP-4981 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4988     TCGA-BP-4989 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-4992     TCGA-BP-4995     TCGA-BP-4998     TCGA-BP-5001 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4870     TCGA-CJ-4875 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4878     TCGA-CJ-4881     TCGA-CJ-4887 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-4889     TCGA-CJ-4890     TCGA-CJ-5671     TCGA-CJ-5675 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-5676     TCGA-CJ-5681     TCGA-CJ-5683     TCGA-CJ-5686 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CW-5585     TCGA-CW-5589 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4857     TCGA-CZ-4858 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5455     TCGA-CZ-5457 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CZ-5459     TCGA-CZ-5462     TCGA-CZ-5463     TCGA-CZ-5466 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5989 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 
    TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5569     TCGA-EU-5904 
"BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" "BCL6 WILD-TYPE" 

Clustering(26) Variable = NFAT5 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        0      0      0
  NFAT5 WILD-TYPE     22     21      3
D26V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  NFAT5 MUTATED        0      0      0      0      0      0      0
  NFAT5 WILD-TYPE      4     10      3     10     10      8      1
D26V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        2      3      1
  NFAT5 WILD-TYPE    188     92    129
D26V3, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             2             188
  CLUS_2             3              92
  CLUS_3             1             129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        2      1      3
  NFAT5 WILD-TYPE     94     52     91
D26V4, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             2              94
  CLUS_2             1              52
  CLUS_3             3              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 CLUS_5 CLUS_6
  NFAT5 MUTATED        0      2      1      0      1      1
  NFAT5 WILD-TYPE     93     54     66     64     67     37
D26V5, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             0              93
  CLUS_2             2              54
  CLUS_3             1              66
  CLUS_4             0              64
  CLUS_5             1              67
  CLUS_6             1              37
[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
  NFAT5 MUTATED        0      3      2
  NFAT5 WILD-TYPE    105    171    105
D26V6, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             0             105
  CLUS_2             3             171
  CLUS_3             2             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        1      1      4
  NFAT5 WILD-TYPE     67    176    166
D26V7, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             1              67
  CLUS_2             1             176
  CLUS_3             4             166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        3      2      1
  NFAT5 WILD-TYPE    111    188    110
D26V8, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             3             111
  CLUS_2             2             188
  CLUS_3             1             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        1      1      4
  NFAT5 WILD-TYPE     94    171    136
D26V9, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             1              94
  CLUS_2             1             171
  CLUS_3             4             136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFAT5 MUTATED        0      1      3      2
  NFAT5 WILD-TYPE    112    100    156     33
D26V10, multiclass
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  CLUS_1             0             112
  CLUS_2             1             100
  CLUS_3             3             156
  CLUS_4             2              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NFAT5 MUTATED        0      0      0      1
  NFAT5 WILD-TYPE     12     20     42     27
D26V11, multiclass
[1] "Remove cluster labels:" "NFAT5 MUTATED"         
clus
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              1             101 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-5466      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-5989      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-EU-5904 
"NFAT5 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  NFAT5 MUTATED        1      0      0
  NFAT5 WILD-TYPE     13     45     43
D26V12, multiclass
[1] "Remove cluster labels:" "NFAT5 MUTATED"         
clus
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              1             101 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-5466      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-CZ-5989      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-EU-5904 
"NFAT5 WILD-TYPE" 

Clustering(27) Variable = LARP1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        0      1      0
  LARP1 WILD-TYPE     22     20      3
D27V1, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              1              45 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3319      TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3323 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3326      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3362 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3365      TCGA-A3-3372      TCGA-A3-3378 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3380      TCGA-A3-3382      TCGA-A3-3383      TCGA-AK-3444 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-AK-3455      TCGA-AK-3456      TCGA-AS-3778      TCGA-B2-3924 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B2-4098      TCGA-B2-4099      TCGA-B8-4143      TCGA-B8-4148 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4620      TCGA-BP-4161 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4167 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4634      TCGA-CJ-4636      TCGA-CJ-4637      TCGA-CJ-4638 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4641      TCGA-CJ-4643 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4644 
"LARP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  LARP1 MUTATED        0      1      0      0      0      0      0
  LARP1 WILD-TYPE      4      9      3     10     10      8      1
D27V2, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              1              45 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3319      TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3323 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3326      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3362 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3365      TCGA-A3-3372      TCGA-A3-3378 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-A3-3380      TCGA-A3-3382      TCGA-A3-3383      TCGA-AK-3444 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-AK-3455      TCGA-AK-3456      TCGA-AS-3778      TCGA-B2-3924 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B2-4098      TCGA-B2-4099      TCGA-B8-4143      TCGA-B8-4148 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4620      TCGA-BP-4161 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4167 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4634      TCGA-CJ-4636      TCGA-CJ-4637      TCGA-CJ-4638 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4641      TCGA-CJ-4643 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4644 
"LARP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        4      0      1
  LARP1 WILD-TYPE    186     95    129
D27V3, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             4             186
  CLUS_2             0              95
  CLUS_3             1             129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        2      1      0
  LARP1 WILD-TYPE     94     52     94
D27V4, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             2              94
  CLUS_2             1              52
  CLUS_3             0              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 CLUS_5 CLUS_6
  LARP1 MUTATED        1      0      1      3      0      0
  LARP1 WILD-TYPE     92     56     66     61     68     38
D27V5, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             1              92
  CLUS_2             0              56
  CLUS_3             1              66
  CLUS_4             3              61
  CLUS_5             0              68
  CLUS_6             0              38
[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
  LARP1 MUTATED        0      3      2
  LARP1 WILD-TYPE    105    171    105
D27V6, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0             105
  CLUS_2             3             171
  CLUS_3             2             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        0      3      2
  LARP1 WILD-TYPE     68    174    168
D27V7, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0              68
  CLUS_2             3             174
  CLUS_3             2             168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        1      3      1
  LARP1 WILD-TYPE    113    187    110
D27V8, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             1             113
  CLUS_2             3             187
  CLUS_3             1             110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        0      3      2
  LARP1 WILD-TYPE     95    169    138
D27V9, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0              95
  CLUS_2             3             169
  CLUS_3             2             138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LARP1 MUTATED        0      1      4      0
  LARP1 WILD-TYPE    112    100    155     35
D27V10, multiclass
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  CLUS_1             0             112
  CLUS_2             1             100
  CLUS_3             4             155
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LARP1 MUTATED        0      0      1      1
  LARP1 WILD-TYPE     12     20     41     27
D27V11, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             100 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5454      TCGA-CZ-5455      TCGA-CZ-5457 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463      TCGA-CZ-5466 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5989 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569      TCGA-EU-5904 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LARP1 MUTATED        1      0      1
  LARP1 WILD-TYPE     13     45     42
D27V12, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             100 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-A3-3387      TCGA-AK-3458 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5454      TCGA-CZ-5455      TCGA-CZ-5457 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CZ-5459      TCGA-CZ-5462      TCGA-CZ-5463      TCGA-CZ-5466 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5989 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569      TCGA-EU-5904 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 

Clustering(28) Variable = KIAA1751 MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        0      0      0
  KIAA1751 WILD-TYPE     22     21      3
D28V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  KIAA1751 MUTATED        0      0      0      0      0      0      0
  KIAA1751 WILD-TYPE      4     10      3     10     10      8      1
D28V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        2      1      3
  KIAA1751 WILD-TYPE    188     94    127
D28V3, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                2                188
  CLUS_2                1                 94
  CLUS_3                3                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        3      0      2
  KIAA1751 WILD-TYPE     93     53     92
D28V4, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                3                 93
  CLUS_2                0                 53
  CLUS_3                2                 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 CLUS_5 CLUS_6
  KIAA1751 MUTATED        2      0      1      2      0      0
  KIAA1751 WILD-TYPE     91     56     66     62     68     38
D28V5, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                2                 91
  CLUS_2                0                 56
  CLUS_3                1                 66
  CLUS_4                2                 62
  CLUS_5                0                 68
  CLUS_6                0                 38
[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
  KIAA1751 MUTATED        2      0      3
  KIAA1751 WILD-TYPE    103    174    104
D28V6, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                2                103
  CLUS_2                0                174
  CLUS_3                3                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        2      2      1
  KIAA1751 WILD-TYPE     66    175    169
D28V7, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                2                 66
  CLUS_2                2                175
  CLUS_3                1                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        1      3      1
  KIAA1751 WILD-TYPE    113    187    110
D28V8, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                1                113
  CLUS_2                3                187
  CLUS_3                1                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        0      4      2
  KIAA1751 WILD-TYPE     95    168    138
D28V9, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                0                 95
  CLUS_2                4                168
  CLUS_3                2                138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1751 MUTATED        0      3      3      0
  KIAA1751 WILD-TYPE    112     98    156     35
D28V10, multiclass
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  CLUS_1                0                112
  CLUS_2                3                 98
  CLUS_3                3                156
  CLUS_4                0                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIAA1751 MUTATED        0      0      1      0
  KIAA1751 WILD-TYPE     12     20     41     28
D28V11, multiclass
[1] "Remove cluster labels:" "KIAA1751 MUTATED"      
clus
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 1                101 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-AK-3458         TCGA-B0-4700         TCGA-B0-4706 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4836         TCGA-B0-4837 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-5080         TCGA-B0-5085 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5399         TCGA-B0-5691 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5692         TCGA-B0-5693         TCGA-B0-5694 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5696         TCGA-B0-5699 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5702         TCGA-B0-5705         TCGA-B0-5709 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-5633         TCGA-B2-5635 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B4-5377         TCGA-B8-4621         TCGA-B8-5545 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-5551         TCGA-B8-5552 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B8-5553         TCGA-BP-4173         TCGA-BP-4340 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4761         TCGA-BP-4770         TCGA-BP-4787 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4789         TCGA-BP-4790         TCGA-BP-4804 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4807         TCGA-BP-4961         TCGA-BP-4967 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4968         TCGA-BP-4970         TCGA-BP-4974 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4976         TCGA-BP-4981         TCGA-BP-4982 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4988         TCGA-BP-4989 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4992         TCGA-BP-4995         TCGA-BP-4998 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-5001         TCGA-BP-5008         TCGA-BP-5009 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-4870         TCGA-CJ-4875         TCGA-CJ-4876 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-4878         TCGA-CJ-4881         TCGA-CJ-4887 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-4889         TCGA-CJ-4890         TCGA-CJ-4895 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5675         TCGA-CJ-5676 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-5681         TCGA-CJ-5683         TCGA-CJ-5686 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-6031         TCGA-CJ-6032         TCGA-CW-5585 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-6087         TCGA-CZ-4854 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-4857         TCGA-CZ-4858         TCGA-CZ-5453 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5455         TCGA-CZ-5457 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5459         TCGA-CZ-5462         TCGA-CZ-5463 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5466         TCGA-CZ-5469         TCGA-CZ-5470 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5989         TCGA-DV-5565         TCGA-DV-5566 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5569         TCGA-EU-5904 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  KIAA1751 MUTATED        0      0      1
  KIAA1751 WILD-TYPE     14     45     42
D28V12, multiclass
[1] "Remove cluster labels:" "KIAA1751 MUTATED"      
clus
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 1                101 
        TCGA-A3-3317         TCGA-A3-3358         TCGA-A3-3387 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-AK-3458         TCGA-B0-4700         TCGA-B0-4706 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4712         TCGA-B0-4810 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-4811         TCGA-B0-4836         TCGA-B0-4837 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-5080         TCGA-B0-5085 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5399         TCGA-B0-5691 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5692         TCGA-B0-5693         TCGA-B0-5694 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5696         TCGA-B0-5699 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B0-5702         TCGA-B0-5705         TCGA-B0-5709 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-5633         TCGA-B2-5635 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B4-5377         TCGA-B8-4621         TCGA-B8-5545 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-5551         TCGA-B8-5552 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B8-5553         TCGA-BP-4173         TCGA-BP-4340 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4761         TCGA-BP-4770         TCGA-BP-4787 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4789         TCGA-BP-4790         TCGA-BP-4804 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4807         TCGA-BP-4961         TCGA-BP-4967 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4968         TCGA-BP-4970         TCGA-BP-4974 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4976         TCGA-BP-4981         TCGA-BP-4982 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4988         TCGA-BP-4989 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-4992         TCGA-BP-4995         TCGA-BP-4998 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-BP-5001         TCGA-BP-5008         TCGA-BP-5009 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-4870         TCGA-CJ-4875         TCGA-CJ-4876 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-4878         TCGA-CJ-4881         TCGA-CJ-4887 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-4889         TCGA-CJ-4890         TCGA-CJ-4895 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5675         TCGA-CJ-5676 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-5681         TCGA-CJ-5683         TCGA-CJ-5686 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CJ-6031         TCGA-CJ-6032         TCGA-CW-5585 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-6087         TCGA-CZ-4854 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-4857         TCGA-CZ-4858         TCGA-CZ-5453 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5455         TCGA-CZ-5457 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5459         TCGA-CZ-5462         TCGA-CZ-5463 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5466         TCGA-CZ-5469         TCGA-CZ-5470 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5989         TCGA-DV-5565         TCGA-DV-5566 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5569         TCGA-EU-5904 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 

Clustering(29) Variable = INSRR MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        0      0      0
  INSRR WILD-TYPE     22     21      3
D29V1, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
  INSRR MUTATED        0      0      0      0      0      0      0
  INSRR WILD-TYPE      4     10      3     10     10      8      1
D29V2, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        2      0      2
  INSRR WILD-TYPE    188     95    128
D29V3, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             2             188
  CLUS_2             0              95
  CLUS_3             2             128
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        0      2      2
  INSRR WILD-TYPE     96     51     92
D29V4, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             0              96
  CLUS_2             2              51
  CLUS_3             2              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 CLUS_5 CLUS_6
  INSRR MUTATED        0      1      2      1      0      0
  INSRR WILD-TYPE     93     55     65     63     68     38
D29V5, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             0              93
  CLUS_2             1              55
  CLUS_3             2              65
  CLUS_4             1              63
  CLUS_5             0              68
  CLUS_6             0              38
[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
  INSRR MUTATED        0      2      2
  INSRR WILD-TYPE    105    172    105
D29V6, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             0             105
  CLUS_2             2             172
  CLUS_3             2             105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        0      1      3
  INSRR WILD-TYPE     68    176    167
D29V7, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             0              68
  CLUS_2             1             176
  CLUS_3             3             167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        2      2      0
  INSRR WILD-TYPE    112    188    111
D29V8, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             2             112
  CLUS_2             2             188
  CLUS_3             0             111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        2      1      1
  INSRR WILD-TYPE     93    171    139
D29V9, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             2              93
  CLUS_2             1             171
  CLUS_3             1             139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  INSRR MUTATED        1      2      1      0
  INSRR WILD-TYPE    111     99    158     35
D29V10, multiclass
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  CLUS_1             1             111
  CLUS_2             2              99
  CLUS_3             1             158
  CLUS_4             0              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  INSRR MUTATED        0      1      0      1
  INSRR WILD-TYPE     12     19     42     27
D29V11, multiclass
[1] "Remove cluster labels:" "INSRR MUTATED"         
clus
  INSRR MUTATED INSRR WILD-TYPE 
              2             100 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-AK-3458      TCGA-B0-4700 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712      TCGA-B0-4810 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837      TCGA-B0-4852 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5399 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693      TCGA-B0-5694 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699      TCGA-B0-5702 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924      TCGA-B2-5633 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5459      TCGA-CZ-5463      TCGA-CZ-5466 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5989 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569      TCGA-EU-5904 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  INSRR MUTATED        0      1      1
  INSRR WILD-TYPE     14     44     42
D29V12, multiclass
[1] "Remove cluster labels:" "INSRR MUTATED"         
clus
  INSRR MUTATED INSRR WILD-TYPE 
              2             100 
     TCGA-A3-3317      TCGA-A3-3358      TCGA-AK-3458      TCGA-B0-4700 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-4706      TCGA-B0-4710      TCGA-B0-4712      TCGA-B0-4810 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4836      TCGA-B0-4837      TCGA-B0-4852 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5080      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5399 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693      TCGA-B0-5694 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5699      TCGA-B0-5702 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5709      TCGA-B2-3924      TCGA-B2-5633 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B2-5635      TCGA-B4-5377      TCGA-B8-4621      TCGA-B8-5545 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4340      TCGA-BP-4761      TCGA-BP-4770 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4789      TCGA-BP-4790      TCGA-BP-4804 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4961      TCGA-BP-4967      TCGA-BP-4968 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4974      TCGA-BP-4976      TCGA-BP-4981 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4982      TCGA-BP-4985      TCGA-BP-4988      TCGA-BP-4989 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-4992      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-5001 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-BP-5008      TCGA-BP-5009      TCGA-CJ-4870      TCGA-CJ-4875 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4887 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4895      TCGA-CJ-5671 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5681      TCGA-CJ-5683 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CW-5585 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CW-5589      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4857 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5459      TCGA-CZ-5463      TCGA-CZ-5466 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5989 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5569      TCGA-EU-5904 
"INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" "INSRR WILD-TYPE" 
