[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"       "-oTGBM-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/GBM-TP/10668124/GBM-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/10686102/transformed.cor.cli.txt"

nPatients in clinical file=598, in cluster file=283, common to both=283
[1]  33 283
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            79            204 
  TP53 MUTATED TP53 WILD-TYPE 
            79            204 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              251 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              251 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           24           259 
  RB1 MUTATED RB1 WILD-TYPE 
           24           259 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           29           254 
  NF1 MUTATED NF1 WILD-TYPE 
           29           254 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            87            196 
  PTEN MUTATED PTEN WILD-TYPE 
            87            196 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            269 
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            269 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              29              254 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              29              254 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             271 
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             271 
[1] "SEMG1 MUTATION ANALYSIS"
[1] 3
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              8             275 
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              8             275 
[1] "RPL5 MUTATION ANALYSIS"
[1] 3
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            276 
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            276 
[1] "SLC26A3 MUTATION ANALYSIS"
[1] 3
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                7               276 
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                7               276 
[1] "MAP3K1 MUTATION ANALYSIS"
[1] 3
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              277 
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               6              277 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            16            267 
  ATRX MUTATED ATRX WILD-TYPE 
            16            267 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             6            277 
  BRAF MUTATED BRAF WILD-TYPE 
             6            277 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            74            209 
  EGFR MUTATED EGFR WILD-TYPE 
            74            209 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11              272 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11              272 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
            8           275 
  KDR MUTATED KDR WILD-TYPE 
            8           275 
[1] "TMPRSS6 MUTATION ANALYSIS"
[1] 3
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               277 
  TMPRSS6 MUTATED TMPRSS6 WILD-TYPE 
                6               277 
[1] "CHD8 MUTATION ANALYSIS"
[1] 3
  CHD8 MUTATED CHD8 WILD-TYPE 
             9            274 
  CHD8 MUTATED CHD8 WILD-TYPE 
             9            274 
[1] "SEMA3C MUTATION ANALYSIS"
[1] 3
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              11              272 
  SEMA3C MUTATED SEMA3C WILD-TYPE 
              11              272 
[1] "ZDHHC4 MUTATION ANALYSIS"
[1] 3
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               3              280 
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               3              280 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             278 
  MMP13 MUTATED MMP13 WILD-TYPE 
              5             278 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             280 
  PRKCD MUTATED PRKCD WILD-TYPE 
              3             280 
[1] "REN MUTATION ANALYSIS"
[1] 3
  REN MUTATED REN WILD-TYPE 
            5           278 
  REN MUTATED REN WILD-TYPE 
            5           278 
[1] "LRRC55 MUTATION ANALYSIS"
[1] 3
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               6              277 
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               6              277 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             22             261 
  MUC17 MUTATED MUC17 WILD-TYPE 
             22             261 
[1] "CD209 MUTATION ANALYSIS"
[1] 3
  CD209 MUTATED CD209 WILD-TYPE 
              5             278 
  CD209 MUTATED CD209 WILD-TYPE 
              5             278 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            279 
  DDX5 MUTATED DDX5 WILD-TYPE 
             4            279 
[1] "TP63 MUTATION ANALYSIS"
[1] 3
  TP63 MUTATED TP63 WILD-TYPE 
             6            277 
  TP63 MUTATED TP63 WILD-TYPE 
             6            277 
[1] "CD1D MUTATION ANALYSIS"
[1] 3
  CD1D MUTATED CD1D WILD-TYPE 
             4            279 
  CD1D MUTATED CD1D WILD-TYPE 
             4            279 
[1] "LZTR1 MUTATION ANALYSIS"
[1] 3
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             10             273 
  LZTR1 MUTATED LZTR1 WILD-TYPE 
             10             273 
[1] "TEX15 MUTATION ANALYSIS"
[1] 3
  TEX15 MUTATED TEX15 WILD-TYPE 
              8             275 
  TEX15 MUTATED TEX15 WILD-TYPE 
              8             275 
[1] "FBN3 MUTATION ANALYSIS"
[1] 3
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            272 
  FBN3 MUTATED FBN3 WILD-TYPE 
            11            272 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"

Input Data has 10 rows and 283 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIR_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 283 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       16     19     11     22
  TP53 WILD-TYPE     53     24     63     32
D1V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           16             53
  CLUS_2           19             24
  CLUS_3           11             63
  CLUS_4           22             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
  TP53 MUTATED       15     30      7     16
  TP53 WILD-TYPE     48     20     41     63
D1V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           15             48
  CLUS_2           30             20
  CLUS_3            7             41
  CLUS_4           16             63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       12     39     10     18
  TP53 WILD-TYPE     65     54     35     42
D1V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             65
  CLUS_2           39             54
  CLUS_3           10             35
  CLUS_4           18             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       47     15     17
  TP53 WILD-TYPE     91     46     59
D1V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           47             91
  CLUS_2           15             46
  CLUS_3           17             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       36     13     29
  TP53 WILD-TYPE     49     94     52
D1V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           36             49
  CLUS_2           13             94
  CLUS_3           29             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
  TP53 MUTATED        5      5     16
  TP53 WILD-TYPE     30     39     13
D1V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            5             30
  CLUS_2            5             39
  CLUS_3           16             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED       12     17      4     10
  TP53 WILD-TYPE     29     21     27     23
D1V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             29
  CLUS_2           17             21
  CLUS_3            4             27
  CLUS_4           10             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       15     22      6
  TP53 WILD-TYPE     33     30     37
D1V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           15             33
  CLUS_2           22             30
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       23     13      8
  TP53 WILD-TYPE     21     49     27
D1V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           23             21
  CLUS_2           13             49
  CLUS_3            8             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED       18     21      5
  TP53 WILD-TYPE     13     65     19
D1V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18             13
  CLUS_2           21             65
  CLUS_3            5             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = PIK3R1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3R1 MUTATED        7      2      8      5
  PIK3R1 WILD-TYPE     62     41     66     49
D2V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               62
  CLUS_2              2               41
  CLUS_3              8               66
  CLUS_4              5               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3R1 MUTATED        7      6      6      3
  PIK3R1 WILD-TYPE     56     44     42     76
D2V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               56
  CLUS_2              6               44
  CLUS_3              6               42
  CLUS_4              3               76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3R1 MUTATED       12     13      4      3
  PIK3R1 WILD-TYPE     65     80     41     57
D2V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             12               65
  CLUS_2             13               80
  CLUS_3              4               41
  CLUS_4              3               57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED       16      5     11
  PIK3R1 WILD-TYPE    122     56     65
D2V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1             16              122
  CLUS_2              5               56
  CLUS_3             11               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED        5     14     12
  PIK3R1 WILD-TYPE     80     93     69
D2V5, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               80
  CLUS_2             14               93
  CLUS_3             12               69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED        7      8      3
  PIK3R1 WILD-TYPE     28     36     26
D2V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               28
  CLUS_2              8               36
  CLUS_3              3               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3R1 MUTATED        7      6      4      5
  PIK3R1 WILD-TYPE     34     32     27     28
D2V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               34
  CLUS_2              6               32
  CLUS_3              4               27
  CLUS_4              5               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
  PIK3R1 MUTATED        9      8      5
  PIK3R1 WILD-TYPE     39     44     38
D2V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              9               39
  CLUS_2              8               44
  CLUS_3              5               38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED        5      6      1
  PIK3R1 WILD-TYPE     39     56     34
D2V9, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               39
  CLUS_2              6               56
  CLUS_3              1               34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3R1 MUTATED        4      8      0
  PIK3R1 WILD-TYPE     27     78     24
D2V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              4               27
  CLUS_2              8               78
  CLUS_3              0               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RB1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED       11      2      3      2
  RB1 WILD-TYPE     58     41     71     52
D3V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          11            58
  CLUS_2           2            41
  CLUS_3           3            71
  CLUS_4           2            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        5      2      0     11
  RB1 WILD-TYPE     58     48     48     68
D3V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           5            58
  CLUS_2           2            48
  CLUS_3           0            48
  CLUS_4          11            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED       11      4      3      6
  RB1 WILD-TYPE     66     89     42     54
D3V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          11            66
  CLUS_2           4            89
  CLUS_3           3            42
  CLUS_4           6            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED       12      6      6
  RB1 WILD-TYPE    126     55     70
D3V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          12           126
  CLUS_2           6            55
  CLUS_3           6            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED       10      4     10
  RB1 WILD-TYPE     75    103     71
D3V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          10            75
  CLUS_2           4           103
  CLUS_3          10            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
  RB1 MUTATED        5      2      1
  RB1 WILD-TYPE     30     42     28
D3V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           5            30
  CLUS_2           2            42
  CLUS_3           1            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RB1 MUTATED        3      1      2      4
  RB1 WILD-TYPE     38     37     29     29
D3V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            38
  CLUS_2           1            37
  CLUS_3           2            29
  CLUS_4           4            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
  RB1 MUTATED        6      2      2
  RB1 WILD-TYPE     42     50     41
D3V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           6            42
  CLUS_2           2            50
  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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      8      1
  RB1 WILD-TYPE     43     54     34
D3V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            43
  CLUS_2           8            54
  CLUS_3           1            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  RB1 MUTATED        1      8      1
  RB1 WILD-TYPE     30     78     23
D3V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            30
  CLUS_2           8            78
  CLUS_3           1            23
[1] 3 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 = NF1 MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED       11      4      4      2
  NF1 WILD-TYPE     58     39     70     52
D4V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          11            58
  CLUS_2           4            39
  CLUS_3           4            70
  CLUS_4           2            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED       14      1      1      5
  NF1 WILD-TYPE     49     49     47     74
D4V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          14            49
  CLUS_2           1            49
  CLUS_3           1            47
  CLUS_4           5            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED       12      3      5      8
  NF1 WILD-TYPE     65     90     40     52
D4V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          12            65
  CLUS_2           3            90
  CLUS_3           5            40
  CLUS_4           8            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED       14      7      7
  NF1 WILD-TYPE    124     54     69
D4V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          14           124
  CLUS_2           7            54
  CLUS_3           7            69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        5      8     16
  NF1 WILD-TYPE     80     99     65
D4V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5            80
  CLUS_2           8            99
  CLUS_3          16            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED       10      2      1
  NF1 WILD-TYPE     25     42     28
D4V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          10            25
  CLUS_2           2            42
  CLUS_3           1            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NF1 MUTATED        7      3      1      5
  NF1 WILD-TYPE     34     35     30     28
D4V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           7            34
  CLUS_2           3            35
  CLUS_3           1            30
  CLUS_4           5            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
  NF1 MUTATED       11      4      1
  NF1 WILD-TYPE     37     48     42
D4V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          11            37
  CLUS_2           4            48
  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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        2      5      4
  NF1 WILD-TYPE     42     57     31
D4V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            42
  CLUS_2           5            57
  CLUS_3           4            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  NF1 MUTATED        1      7      3
  NF1 WILD-TYPE     30     79     21
D4V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            30
  CLUS_2           7            79
  CLUS_3           3            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED       25     10     18     22
  PTEN WILD-TYPE     44     33     56     32
D5V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           25             44
  CLUS_2           10             33
  CLUS_3           18             56
  CLUS_4           22             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       18     16      9     32
  PTEN WILD-TYPE     45     34     39     47
D5V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           18             45
  CLUS_2           16             34
  CLUS_3            9             39
  CLUS_4           32             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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       30     19     18     20
  PTEN WILD-TYPE     47     74     27     40
D5V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           30             47
  CLUS_2           19             74
  CLUS_3           18             27
  CLUS_4           20             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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       45     21     21
  PTEN WILD-TYPE     93     40     55
D5V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           45             93
  CLUS_2           21             40
  CLUS_3           21             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED       31     29     25
  PTEN WILD-TYPE     54     78     56
D5V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           31             54
  CLUS_2           29             78
  CLUS_3           25             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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       10     15      8
  PTEN WILD-TYPE     25     29     21
D5V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           10             25
  CLUS_2           15             29
  CLUS_3            8             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED       12     14      6     12
  PTEN WILD-TYPE     29     24     25     21
D5V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           12             29
  CLUS_2           14             24
  CLUS_3            6             25
  CLUS_4           12             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED       20     13     11
  PTEN WILD-TYPE     28     39     32
D5V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           20             28
  CLUS_2           13             39
  CLUS_3           11             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED       10     23     12
  PTEN WILD-TYPE     34     39     23
D5V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           10             34
  CLUS_2           23             39
  CLUS_3           12             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table 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        8     28      9
  PTEN WILD-TYPE     23     58     15
D5V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            8             23
  CLUS_2           28             58
  CLUS_3            9             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = IDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        1      3      0      9
  IDH1 WILD-TYPE     68     40     74     45
D6V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            3             40
  CLUS_3            0             74
  CLUS_4            9             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        0     13      0      0
  IDH1 WILD-TYPE     63     37     48     79
D6V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             63
  CLUS_2           13             37
  CLUS_3            0             48
  CLUS_4            0             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        0     13      1      0
  IDH1 WILD-TYPE     77     80     44     60
D6V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             77
  CLUS_2           13             80
  CLUS_3            1             44
  CLUS_4            0             60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED       13      0      1
  IDH1 WILD-TYPE    125     61     75
D6V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           13            125
  CLUS_2            0             61
  CLUS_3            1             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        1      0     12
  IDH1 WILD-TYPE     84    107     69
D6V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             84
  CLUS_2            0            107
  CLUS_3           12             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        0      0      5
  IDH1 WILD-TYPE     35     44     24
D6V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             35
  CLUS_2            0             44
  CLUS_3            5             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        1      6      0      0
  IDH1 WILD-TYPE     40     32     31     33
D6V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             40
  CLUS_2            6             32
  CLUS_3            0             31
  CLUS_4            0             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
  IDH1 MUTATED        0      7      0
  IDH1 WILD-TYPE     48     45     43
D6V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             48
  CLUS_2            7             45
  CLUS_3            0             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        7      0      1
  IDH1 WILD-TYPE     37     62     34
D6V9, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            7             37
  CLUS_2            0             62
  CLUS_3            1             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        8      0      0
  IDH1 WILD-TYPE     23     86     24
D6V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            8             23
  CLUS_2            0             86
  CLUS_3            0             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        6      6      9      5
  PIK3CA WILD-TYPE     63     37     65     49
D7V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               63
  CLUS_2              6               37
  CLUS_3              9               65
  CLUS_4              5               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        8      6      8      4
  PIK3CA WILD-TYPE     55     44     40     75
D7V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               55
  CLUS_2              6               44
  CLUS_3              8               40
  CLUS_4              4               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger 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        9     11      2      6
  PIK3CA WILD-TYPE     68     82     43     54
D7V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9               68
  CLUS_2             11               82
  CLUS_3              2               43
  CLUS_4              6               54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED       14      6      8
  PIK3CA WILD-TYPE    124     55     68
D7V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             14              124
  CLUS_2              6               55
  CLUS_3              8               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
  PIK3CA MUTATED        8     10      9
  PIK3CA WILD-TYPE     77     97     72
D7V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               77
  CLUS_2             10               97
  CLUS_3              9               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
  PIK3CA MUTATED        2      5      6
  PIK3CA WILD-TYPE     33     39     23
D7V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               33
  CLUS_2              5               39
  CLUS_3              6               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PIK3CA MUTATED        3      5      2      4
  PIK3CA WILD-TYPE     38     33     29     29
D7V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               38
  CLUS_2              5               33
  CLUS_3              2               29
  CLUS_4              4               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
  PIK3CA MUTATED        7      5      2
  PIK3CA WILD-TYPE     41     47     41
D7V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               41
  CLUS_2              5               47
  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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        6      3      2
  PIK3CA WILD-TYPE     38     59     33
D7V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               38
  CLUS_2              3               59
  CLUS_3              2               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PIK3CA MUTATED        4      7      0
  PIK3CA WILD-TYPE     27     79     24
D7V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               27
  CLUS_2              7               79
  CLUS_3              0               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = STAG2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        4      3      1      2
  STAG2 WILD-TYPE     65     40     73     52
D8V1, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             4              65
  CLUS_2             3              40
  CLUS_3             1              73
  CLUS_4             2              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        2      1      3      4
  STAG2 WILD-TYPE     61     49     45     75
D8V2, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              61
  CLUS_2             1              49
  CLUS_3             3              45
  CLUS_4             4              75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        4      5      2      1
  STAG2 WILD-TYPE     73     88     43     59
D8V3, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             4              73
  CLUS_2             5              88
  CLUS_3             2              43
  CLUS_4             1              59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        5      2      5
  STAG2 WILD-TYPE    133     59     71
D8V4, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             5             133
  CLUS_2             2              59
  CLUS_3             5              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
  STAG2 MUTATED        5      4      3
  STAG2 WILD-TYPE     80    103     78
D8V5, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             5              80
  CLUS_2             4             103
  CLUS_3             3              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
  STAG2 MUTATED        1      3      1
  STAG2 WILD-TYPE     34     41     28
D8V6, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             1              34
  CLUS_2             3              41
  CLUS_3             1              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  STAG2 MUTATED        0      2      0      5
  STAG2 WILD-TYPE     41     36     31     28
D8V7, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              36
  CLUS_3             0              31
  CLUS_4             5              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
  STAG2 MUTATED        4      2      1
  STAG2 WILD-TYPE     44     50     42
D8V8, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             4              44
  CLUS_2             2              50
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        1      3      3
  STAG2 WILD-TYPE     43     59     32
D8V9, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             1              43
  CLUS_2             3              59
  CLUS_3             3              32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  STAG2 MUTATED        0      4      3
  STAG2 WILD-TYPE     31     82     21
D8V10, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             0              31
  CLUS_2             4              82
  CLUS_3             3              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = SEMG1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMG1 MUTATED        1      1      4      2
  SEMG1 WILD-TYPE     68     42     70     52
D9V1, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             1              68
  CLUS_2             1              42
  CLUS_3             4              70
  CLUS_4             2              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMG1 MUTATED        0      2      1      5
  SEMG1 WILD-TYPE     63     48     47     74
D9V2, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             0              63
  CLUS_2             2              48
  CLUS_3             1              47
  CLUS_4             5              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMG1 MUTATED        2      4      1      1
  SEMG1 WILD-TYPE     75     89     44     59
D9V3, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             2              75
  CLUS_2             4              89
  CLUS_3             1              44
  CLUS_4             1              59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SEMG1 MUTATED        4      2      2
  SEMG1 WILD-TYPE    134     59     74
D9V4, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             4             134
  CLUS_2             2              59
  CLUS_3             2              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SEMG1 MUTATED        3      5      0
  SEMG1 WILD-TYPE     82    102     81
D9V5, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             3              82
  CLUS_2             5             102
  CLUS_3             0              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SEMG1 MUTATED        0      1      0
  SEMG1 WILD-TYPE     35     43     29
D9V6, multiclass
[1] "Remove cluster labels:" "SEMG1 MUTATED"         
clus
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              1             107 
     TCGA-06-0650      TCGA-06-1804      TCGA-06-1806      TCGA-06-5408 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6699      TCGA-06-6700      TCGA-06-6701      TCGA-12-5295 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-12-5299      TCGA-12-5301      TCGA-14-0740      TCGA-14-0781 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-14-0862      TCGA-14-1043      TCGA-14-1395      TCGA-14-1450 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-15-1444      TCGA-19-5947      TCGA-19-5950      TCGA-19-5951 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5952      TCGA-19-5953      TCGA-19-5954      TCGA-19-5955 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5958      TCGA-19-5959      TCGA-19-5960      TCGA-26-1442 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-26-5132      TCGA-26-5133      TCGA-26-5134      TCGA-26-5135 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-26-5136      TCGA-26-5139      TCGA-26-6173      TCGA-26-6174 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-28-2501      TCGA-28-2510      TCGA-28-5204      TCGA-28-5207 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5211      TCGA-28-5213 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-28-5214      TCGA-28-5215      TCGA-28-5216      TCGA-28-5218 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-28-5219      TCGA-28-5220      TCGA-28-6450      TCGA-32-1980 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-32-5222      TCGA-41-5651      TCGA-41-6646      TCGA-74-6573 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-74-6575      TCGA-74-6577      TCGA-74-6578      TCGA-74-6584 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4925      TCGA-76-4926      TCGA-76-4927      TCGA-76-4928 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4929      TCGA-76-4931      TCGA-76-4932      TCGA-76-4934 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4935      TCGA-76-6191      TCGA-76-6192      TCGA-76-6193 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6280      TCGA-76-6282      TCGA-76-6283      TCGA-76-6285 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6286      TCGA-76-6656      TCGA-76-6657      TCGA-76-6660 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6661      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-81-5910      TCGA-81-5911      TCGA-87-5896 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMG1 MUTATED        0      1      1      0
  SEMG1 WILD-TYPE     41     37     30     33
D9V7, multiclass
[1] "Remove cluster labels:" "SEMG1 MUTATED"         
clus
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              2             141 
     TCGA-02-0003      TCGA-02-2470      TCGA-02-2485      TCGA-06-0126 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0128      TCGA-06-0129      TCGA-06-0130      TCGA-06-0154 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0155      TCGA-06-0189      TCGA-06-0238      TCGA-06-0644 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0650      TCGA-06-0875      TCGA-06-0877      TCGA-06-0878 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0879      TCGA-06-0882      TCGA-06-0939      TCGA-06-1804 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-1806      TCGA-06-2557      TCGA-06-2558      TCGA-06-2559 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-2562      TCGA-06-2563      TCGA-06-2564      TCGA-06-2565 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-2567      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-06-6388      TCGA-06-6389 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6390      TCGA-06-6391      TCGA-06-6693      TCGA-06-6694 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6695      TCGA-06-6697      TCGA-06-6698      TCGA-06-6699 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6700      TCGA-06-6701      TCGA-08-0386      TCGA-12-0692 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-12-1597      TCGA-12-3649      TCGA-12-3650      TCGA-12-3652 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-12-3653      TCGA-12-5295      TCGA-12-5301      TCGA-14-0813 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-14-0862      TCGA-14-0871      TCGA-14-1823      TCGA-16-0846 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-1390      TCGA-19-1790      TCGA-19-2619      TCGA-19-2620 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-2625      TCGA-19-2631      TCGA-19-4068      TCGA-19-5947 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5950      TCGA-19-5951      TCGA-19-5952      TCGA-19-5953 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5954      TCGA-19-5955      TCGA-19-5958      TCGA-19-5959 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5960      TCGA-26-1442      TCGA-26-5132      TCGA-26-5133 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-26-5134      TCGA-26-6173      TCGA-26-6174      TCGA-27-1830 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1833      TCGA-27-1834 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-27-1836      TCGA-27-2518      TCGA-27-2528      TCGA-28-1747 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2501      TCGA-28-5208      TCGA-28-5214 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-32-1970      TCGA-32-1982      TCGA-32-1986      TCGA-32-1991 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-32-4210      TCGA-32-4211      TCGA-32-5222      TCGA-41-2573 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-41-3392      TCGA-41-3393      TCGA-41-3915      TCGA-41-4097 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-41-5651      TCGA-41-6646      TCGA-74-6573      TCGA-74-6575 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-74-6577      TCGA-74-6578      TCGA-74-6584      TCGA-76-4926 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4927      TCGA-76-4928      TCGA-76-4929      TCGA-76-4931 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4932      TCGA-76-6192      TCGA-76-6193      TCGA-76-6282 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6283      TCGA-76-6285      TCGA-76-6656      TCGA-76-6657 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6660      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-81-5910 
"SEMG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SEMG1 MUTATED        0      1      1
  SEMG1 WILD-TYPE     48     51     42
D9V8, multiclass
[1] "Remove cluster labels:" "SEMG1 MUTATED"         
clus
  SEMG1 MUTATED SEMG1 WILD-TYPE 
              2             141 
     TCGA-02-0003      TCGA-02-2470      TCGA-02-2485      TCGA-06-0126 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0128      TCGA-06-0129      TCGA-06-0130      TCGA-06-0154 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0155      TCGA-06-0189      TCGA-06-0238      TCGA-06-0644 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0650      TCGA-06-0875      TCGA-06-0877      TCGA-06-0878 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-0879      TCGA-06-0882      TCGA-06-0939      TCGA-06-1804 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-1806      TCGA-06-2557      TCGA-06-2558      TCGA-06-2559 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-2562      TCGA-06-2563      TCGA-06-2564      TCGA-06-2565 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-2567      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-06-6388      TCGA-06-6389 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6390      TCGA-06-6391      TCGA-06-6693      TCGA-06-6694 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6695      TCGA-06-6697      TCGA-06-6698      TCGA-06-6699 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-06-6700      TCGA-06-6701      TCGA-08-0386      TCGA-12-0692 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-12-1597      TCGA-12-3649      TCGA-12-3650      TCGA-12-3652 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-12-3653      TCGA-12-5295      TCGA-12-5301      TCGA-14-0813 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-14-0862      TCGA-14-0871      TCGA-14-1823      TCGA-16-0846 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-1390      TCGA-19-1790      TCGA-19-2619      TCGA-19-2620 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-2625      TCGA-19-2631      TCGA-19-4068      TCGA-19-5947 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5950      TCGA-19-5951      TCGA-19-5952      TCGA-19-5953 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5954      TCGA-19-5955      TCGA-19-5958      TCGA-19-5959 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-19-5960      TCGA-26-1442      TCGA-26-5132      TCGA-26-5133 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-26-5134      TCGA-26-6173      TCGA-26-6174      TCGA-27-1830 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1833      TCGA-27-1834 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-27-1836      TCGA-27-2518      TCGA-27-2528      TCGA-28-1747 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2501      TCGA-28-5208      TCGA-28-5214 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-32-1970      TCGA-32-1982      TCGA-32-1986      TCGA-32-1991 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-32-4210      TCGA-32-4211      TCGA-32-5222      TCGA-41-2573 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-41-3392      TCGA-41-3393      TCGA-41-3915      TCGA-41-4097 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-41-5651      TCGA-41-6646      TCGA-74-6573      TCGA-74-6575 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-74-6577      TCGA-74-6578      TCGA-74-6584      TCGA-76-4926 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4927      TCGA-76-4928      TCGA-76-4929      TCGA-76-4931 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-4932      TCGA-76-6192      TCGA-76-6193      TCGA-76-6282 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6283      TCGA-76-6285      TCGA-76-6656      TCGA-76-6657 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-76-6660      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" "SEMG1 WILD-TYPE" 
     TCGA-81-5910 
"SEMG1 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SEMG1 MUTATED        1      1      1
  SEMG1 WILD-TYPE     43     61     34
D9V9, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             1              43
  CLUS_2             1              61
  CLUS_3             1              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  SEMG1 MUTATED        1      1      1
  SEMG1 WILD-TYPE     30     85     23
D9V10, multiclass
        clus
vv       SEMG1 MUTATED SEMG1 WILD-TYPE
  CLUS_1             1              30
  CLUS_2             1              85
  CLUS_3             1              23
[1] 3 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 = RPL5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPL5 MUTATED        1      2      3      0
  RPL5 WILD-TYPE     68     41     71     54
D10V1, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            2             41
  CLUS_3            3             71
  CLUS_4            0             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPL5 MUTATED        3      0      1      2
  RPL5 WILD-TYPE     60     50     47     77
D10V2, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            3             60
  CLUS_2            0             50
  CLUS_3            1             47
  CLUS_4            2             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPL5 MUTATED        1      3      1      2
  RPL5 WILD-TYPE     76     90     44     58
D10V3, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            1             76
  CLUS_2            3             90
  CLUS_3            1             44
  CLUS_4            2             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPL5 MUTATED        3      3      1
  RPL5 WILD-TYPE    135     58     75
D10V4, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            3            135
  CLUS_2            3             58
  CLUS_3            1             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPL5 MUTATED        2      3      2
  RPL5 WILD-TYPE     83    104     79
D10V5, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            2             83
  CLUS_2            3            104
  CLUS_3            2             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPL5 MUTATED        1      1      1
  RPL5 WILD-TYPE     34     43     28
D10V6, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            1             34
  CLUS_2            1             43
  CLUS_3            1             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  RPL5 MUTATED        2      1      1      0
  RPL5 WILD-TYPE     39     37     30     33
D10V7, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            2             39
  CLUS_2            1             37
  CLUS_3            1             30
  CLUS_4            0             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
  RPL5 MUTATED        1      1      2
  RPL5 WILD-TYPE     47     51     41
D10V8, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            1             47
  CLUS_2            1             51
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPL5 MUTATED        2      1      0
  RPL5 WILD-TYPE     42     61     35
D10V9, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            2             42
  CLUS_2            1             61
  CLUS_3            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  RPL5 MUTATED        1      2      0
  RPL5 WILD-TYPE     30     84     24
D10V10, multiclass
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  CLUS_1            1             30
  CLUS_2            2             84
  CLUS_3            0             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = SLC26A3 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC26A3 MUTATED        1      1      2      2
  SLC26A3 WILD-TYPE     68     42     72     52
D11V1, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               1                68
  CLUS_2               1                42
  CLUS_3               2                72
  CLUS_4               2                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC26A3 MUTATED        2      1      2      1
  SLC26A3 WILD-TYPE     61     49     46     78
D11V2, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               2                61
  CLUS_2               1                49
  CLUS_3               2                46
  CLUS_4               1                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC26A3 MUTATED        1      4      0      2
  SLC26A3 WILD-TYPE     76     89     45     58
D11V3, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               1                76
  CLUS_2               4                89
  CLUS_3               0                45
  CLUS_4               2                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC26A3 MUTATED        4      0      3
  SLC26A3 WILD-TYPE    134     61     73
D11V4, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               4               134
  CLUS_2               0                61
  CLUS_3               3                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
  SLC26A3 MUTATED        2      4      1
  SLC26A3 WILD-TYPE     83    103     80
D11V5, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               2                83
  CLUS_2               4               103
  CLUS_3               1                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC26A3 MUTATED        0      1      1
  SLC26A3 WILD-TYPE     35     43     28
D11V6, multiclass
[1] "Remove cluster labels:" "SLC26A3 MUTATED"       
clus
  SLC26A3 MUTATED SLC26A3 WILD-TYPE 
                2               106 
       TCGA-06-0650        TCGA-06-1804        TCGA-06-1806        TCGA-06-5408 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-06-5410        TCGA-06-5411        TCGA-06-5412        TCGA-06-5413 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-06-5414        TCGA-06-5415        TCGA-06-5417        TCGA-06-5418 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-06-5856        TCGA-06-5858        TCGA-06-5859        TCGA-06-6388 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-06-6389        TCGA-06-6390        TCGA-06-6391        TCGA-06-6693 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-06-6694        TCGA-06-6695        TCGA-06-6697        TCGA-06-6698 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-06-6699        TCGA-06-6700        TCGA-06-6701        TCGA-12-5295 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-12-5299        TCGA-12-5301        TCGA-14-0740        TCGA-14-0781 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-14-0862        TCGA-14-1043        TCGA-14-1395        TCGA-14-1450 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-15-1444        TCGA-19-5947        TCGA-19-5950        TCGA-19-5951 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-19-5952        TCGA-19-5953        TCGA-19-5954        TCGA-19-5955 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-19-5958        TCGA-19-5959        TCGA-19-5960        TCGA-26-1442 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-26-5132        TCGA-26-5133        TCGA-26-5134        TCGA-26-5135 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-26-5136        TCGA-26-5139        TCGA-26-6173        TCGA-26-6174 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-28-2501        TCGA-28-2510        TCGA-28-5204        TCGA-28-5207 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-28-5208        TCGA-28-5209        TCGA-28-5211        TCGA-28-5213 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-28-5214        TCGA-28-5215        TCGA-28-5218        TCGA-28-5219 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-28-5220        TCGA-28-6450        TCGA-32-1979        TCGA-32-1980 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-32-5222        TCGA-41-5651        TCGA-41-6646        TCGA-74-6573 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-74-6575        TCGA-74-6577        TCGA-74-6578        TCGA-74-6584 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-76-4925        TCGA-76-4926        TCGA-76-4927        TCGA-76-4928 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-76-4929        TCGA-76-4931        TCGA-76-4932        TCGA-76-4934 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-76-4935        TCGA-76-6191        TCGA-76-6192        TCGA-76-6193 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-76-6280        TCGA-76-6282        TCGA-76-6283        TCGA-76-6285 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-76-6286        TCGA-76-6656        TCGA-76-6657        TCGA-76-6661 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-76-6662        TCGA-76-6663        TCGA-76-6664        TCGA-81-5910 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
       TCGA-81-5911        TCGA-87-5896 
"SLC26A3 WILD-TYPE" "SLC26A3 WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SLC26A3 MUTATED        3      0      1      0
  SLC26A3 WILD-TYPE     38     38     30     33
D11V7, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               3                38
  CLUS_2               0                38
  CLUS_3               1                30
  CLUS_4               0                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
  SLC26A3 MUTATED        3      0      1
  SLC26A3 WILD-TYPE     45     52     42
D11V8, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               3                45
  CLUS_2               0                52
  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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC26A3 MUTATED        2      0      2
  SLC26A3 WILD-TYPE     42     62     33
D11V9, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               2                42
  CLUS_2               0                62
  CLUS_3               2                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  SLC26A3 MUTATED        2      1      1
  SLC26A3 WILD-TYPE     29     85     23
D11V10, multiclass
        clus
vv       SLC26A3 MUTATED SLC26A3 WILD-TYPE
  CLUS_1               2                29
  CLUS_2               1                85
  CLUS_3               1                23
[1] 3 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 = MAP3K1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP3K1 MUTATED        1      1      2      1
  MAP3K1 WILD-TYPE     68     42     72     53
D12V1, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              1               68
  CLUS_2              1               42
  CLUS_3              2               72
  CLUS_4              1               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP3K1 MUTATED        1      1      2      1
  MAP3K1 WILD-TYPE     62     49     46     78
D12V2, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              1               62
  CLUS_2              1               49
  CLUS_3              2               46
  CLUS_4              1               78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP3K1 MUTATED        2      2      0      2
  MAP3K1 WILD-TYPE     75     91     45     58
D12V3, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              2               75
  CLUS_2              2               91
  CLUS_3              0               45
  CLUS_4              2               58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAP3K1 MUTATED        2      2      2
  MAP3K1 WILD-TYPE    136     59     74
D12V4, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              2              136
  CLUS_2              2               59
  CLUS_3              2               74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAP3K1 MUTATED        2      2      2
  MAP3K1 WILD-TYPE     83    105     79
D12V5, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              2               83
  CLUS_2              2              105
  CLUS_3              2               79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAP3K1 MUTATED        1      0      0
  MAP3K1 WILD-TYPE     34     44     29
D12V6, multiclass
[1] "Remove cluster labels:" "MAP3K1 MUTATED"        
clus
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               1              107 
      TCGA-06-0650       TCGA-06-1804       TCGA-06-1806       TCGA-06-5408 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6388 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6389       TCGA-06-6390       TCGA-06-6391       TCGA-06-6693 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6694       TCGA-06-6695       TCGA-06-6697       TCGA-06-6698 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6699       TCGA-06-6700       TCGA-06-6701       TCGA-12-5295 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-12-5299       TCGA-12-5301       TCGA-14-0740       TCGA-14-0781 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-14-0862       TCGA-14-1043       TCGA-14-1395       TCGA-14-1450 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-15-1444       TCGA-19-5947       TCGA-19-5950       TCGA-19-5951 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5952       TCGA-19-5953       TCGA-19-5954       TCGA-19-5955 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5958       TCGA-19-5959       TCGA-19-5960       TCGA-26-1442 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-26-5132       TCGA-26-5133       TCGA-26-5134       TCGA-26-5135 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-26-5136       TCGA-26-5139       TCGA-26-6174       TCGA-28-2501 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-28-2510       TCGA-28-5204       TCGA-28-5207       TCGA-28-5208 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-28-5209       TCGA-28-5211       TCGA-28-5213       TCGA-28-5214 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-28-5215       TCGA-28-5216       TCGA-28-5218       TCGA-28-5219 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-28-5220       TCGA-28-6450       TCGA-32-1979       TCGA-32-1980 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-32-5222       TCGA-41-5651       TCGA-41-6646       TCGA-74-6573 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-74-6575       TCGA-74-6577       TCGA-74-6578       TCGA-74-6584 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4925       TCGA-76-4926       TCGA-76-4927       TCGA-76-4928 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4929       TCGA-76-4931       TCGA-76-4932       TCGA-76-4934 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4935       TCGA-76-6191       TCGA-76-6192       TCGA-76-6193 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6280       TCGA-76-6282       TCGA-76-6283       TCGA-76-6285 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6286       TCGA-76-6656       TCGA-76-6657       TCGA-76-6660 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6661       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-81-5910       TCGA-81-5911       TCGA-87-5896 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MAP3K1 MUTATED        0      0      0      2
  MAP3K1 WILD-TYPE     41     38     31     31
D12V7, multiclass
[1] "Remove cluster labels:" "MAP3K1 MUTATED"        
clus
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               2              141 
      TCGA-02-0003       TCGA-02-2470       TCGA-02-2485       TCGA-06-0126 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0128       TCGA-06-0129       TCGA-06-0130       TCGA-06-0154 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0155       TCGA-06-0189       TCGA-06-0238       TCGA-06-0644 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0650       TCGA-06-0875       TCGA-06-0876       TCGA-06-0877 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0879       TCGA-06-0882       TCGA-06-0939 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-1804       TCGA-06-1806       TCGA-06-2557       TCGA-06-2558 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5414 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5415       TCGA-06-5417       TCGA-06-5418       TCGA-06-5856 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5858       TCGA-06-5859       TCGA-06-6388       TCGA-06-6389 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6390       TCGA-06-6391       TCGA-06-6693       TCGA-06-6694 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6695       TCGA-06-6697       TCGA-06-6698       TCGA-06-6699 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6700       TCGA-06-6701       TCGA-08-0386       TCGA-12-0692 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-12-1597       TCGA-12-3649       TCGA-12-3650       TCGA-12-3652 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-12-3653       TCGA-12-5295       TCGA-12-5301       TCGA-14-0813 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-14-0862       TCGA-14-0871       TCGA-14-1823       TCGA-16-0846 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-1390       TCGA-19-1790       TCGA-19-2619       TCGA-19-2620 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-2625       TCGA-19-2631       TCGA-19-4068       TCGA-19-5947 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5950       TCGA-19-5951       TCGA-19-5952       TCGA-19-5953 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5954       TCGA-19-5955       TCGA-19-5958       TCGA-19-5959 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1442       TCGA-26-5132       TCGA-26-5133 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-26-5134       TCGA-26-6174       TCGA-27-1830       TCGA-27-1831 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-27-1832       TCGA-27-1833       TCGA-27-1834       TCGA-27-1836 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-27-2518       TCGA-27-2528       TCGA-28-1747       TCGA-28-1753 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-28-2501       TCGA-28-5208       TCGA-28-5214       TCGA-32-1970 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-32-1982       TCGA-32-1986       TCGA-32-1991       TCGA-32-4210 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-32-4211       TCGA-32-5222       TCGA-41-2573       TCGA-41-2575 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-41-3392       TCGA-41-3393       TCGA-41-3915       TCGA-41-4097 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-41-5651       TCGA-41-6646       TCGA-74-6573       TCGA-74-6575 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-74-6577       TCGA-74-6578       TCGA-74-6584       TCGA-76-4926 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4927       TCGA-76-4928       TCGA-76-4929       TCGA-76-4931 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4932       TCGA-76-6192       TCGA-76-6193       TCGA-76-6282 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6283       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6660       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-81-5910 
"MAP3K1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAP3K1 MUTATED        1      1      0
  MAP3K1 WILD-TYPE     47     51     43
D12V8, multiclass
[1] "Remove cluster labels:" "MAP3K1 MUTATED"        
clus
  MAP3K1 MUTATED MAP3K1 WILD-TYPE 
               2              141 
      TCGA-02-0003       TCGA-02-2470       TCGA-02-2485       TCGA-06-0126 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0128       TCGA-06-0129       TCGA-06-0130       TCGA-06-0154 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0155       TCGA-06-0189       TCGA-06-0238       TCGA-06-0644 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0650       TCGA-06-0875       TCGA-06-0876       TCGA-06-0877 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0879       TCGA-06-0882       TCGA-06-0939 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-1804       TCGA-06-1806       TCGA-06-2557       TCGA-06-2558 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5414 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5415       TCGA-06-5417       TCGA-06-5418       TCGA-06-5856 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-5858       TCGA-06-5859       TCGA-06-6388       TCGA-06-6389 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6390       TCGA-06-6391       TCGA-06-6693       TCGA-06-6694 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6695       TCGA-06-6697       TCGA-06-6698       TCGA-06-6699 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-06-6700       TCGA-06-6701       TCGA-08-0386       TCGA-12-0692 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-12-1597       TCGA-12-3649       TCGA-12-3650       TCGA-12-3652 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-12-3653       TCGA-12-5295       TCGA-12-5301       TCGA-14-0813 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-14-0862       TCGA-14-0871       TCGA-14-1823       TCGA-16-0846 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-1390       TCGA-19-1790       TCGA-19-2619       TCGA-19-2620 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-2625       TCGA-19-2631       TCGA-19-4068       TCGA-19-5947 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5950       TCGA-19-5951       TCGA-19-5952       TCGA-19-5953 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5954       TCGA-19-5955       TCGA-19-5958       TCGA-19-5959 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1442       TCGA-26-5132       TCGA-26-5133 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-26-5134       TCGA-26-6174       TCGA-27-1830       TCGA-27-1831 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-27-1832       TCGA-27-1833       TCGA-27-1834       TCGA-27-1836 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-27-2518       TCGA-27-2528       TCGA-28-1747       TCGA-28-1753 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-28-2501       TCGA-28-5208       TCGA-28-5214       TCGA-32-1970 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-32-1982       TCGA-32-1986       TCGA-32-1991       TCGA-32-4210 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-32-4211       TCGA-32-5222       TCGA-41-2573       TCGA-41-2575 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-41-3392       TCGA-41-3393       TCGA-41-3915       TCGA-41-4097 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-41-5651       TCGA-41-6646       TCGA-74-6573       TCGA-74-6575 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-74-6577       TCGA-74-6578       TCGA-74-6584       TCGA-76-4926 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4927       TCGA-76-4928       TCGA-76-4929       TCGA-76-4931 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-4932       TCGA-76-6192       TCGA-76-6193       TCGA-76-6282 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6283       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-76-6660       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" "MAP3K1 WILD-TYPE" 
      TCGA-81-5910 
"MAP3K1 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAP3K1 MUTATED        1      3      0
  MAP3K1 WILD-TYPE     43     59     35
D12V9, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              1               43
  CLUS_2              3               59
  CLUS_3              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  MAP3K1 MUTATED        1      3      0
  MAP3K1 WILD-TYPE     30     83     24
D12V10, multiclass
        clus
vv       MAP3K1 MUTATED MAP3K1 WILD-TYPE
  CLUS_1              1               30
  CLUS_2              3               83
  CLUS_3              0               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = ATRX MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED        2      4      0      7
  ATRX WILD-TYPE     67     39     74     47
D13V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            2             67
  CLUS_2            4             39
  CLUS_3            0             74
  CLUS_4            7             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED        0     11      0      2
  ATRX WILD-TYPE     63     39     48     77
D13V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            0             63
  CLUS_2           11             39
  CLUS_3            0             48
  CLUS_4            2             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED        2     11      3      0
  ATRX WILD-TYPE     75     82     42     60
D13V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            2             75
  CLUS_2           11             82
  CLUS_3            3             42
  CLUS_4            0             60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED       13      0      3
  ATRX WILD-TYPE    125     61     73
D13V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           13            125
  CLUS_2            0             61
  CLUS_3            3             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
  ATRX MUTATED        1      1     13
  ATRX WILD-TYPE     84    106     68
D13V5, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1             84
  CLUS_2            1            106
  CLUS_3           13             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
  ATRX MUTATED        2      1      4
  ATRX WILD-TYPE     33     43     25
D13V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            2             33
  CLUS_2            1             43
  CLUS_3            4             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ATRX MUTATED        0      6      0      2
  ATRX WILD-TYPE     41     32     31     31
D13V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            0             41
  CLUS_2            6             32
  CLUS_3            0             31
  CLUS_4            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED        2      6      0
  ATRX WILD-TYPE     46     46     43
D13V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            2             46
  CLUS_2            6             46
  CLUS_3            0             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED        7      1      0
  ATRX WILD-TYPE     37     61     35
D13V9, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            7             37
  CLUS_2            1             61
  CLUS_3            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  ATRX MUTATED        7      1      0
  ATRX WILD-TYPE     24     85     24
D13V10, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            7             24
  CLUS_2            1             85
  CLUS_3            0             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = BRAF MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        1      1      2      0
  BRAF WILD-TYPE     68     42     72     54
D14V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             68
  CLUS_2            1             42
  CLUS_3            2             72
  CLUS_4            0             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        2      0      1      1
  BRAF WILD-TYPE     61     50     47     78
D14V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             61
  CLUS_2            0             50
  CLUS_3            1             47
  CLUS_4            1             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        2      1      0      3
  BRAF WILD-TYPE     75     92     45     57
D14V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             75
  CLUS_2            1             92
  CLUS_3            0             45
  CLUS_4            3             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        2      4      0
  BRAF WILD-TYPE    136     57     76
D14V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2            136
  CLUS_2            4             57
  CLUS_3            0             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      2      3
  BRAF WILD-TYPE     84    105     78
D14V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             84
  CLUS_2            2            105
  CLUS_3            3             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
  BRAF MUTATED        2      0      0
  BRAF WILD-TYPE     33     44     29
D14V6, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             2            106 
    TCGA-06-0650     TCGA-06-1804     TCGA-06-5408     TCGA-06-5410 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-06-6388     TCGA-06-6389 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-6390     TCGA-06-6391     TCGA-06-6693     TCGA-06-6694 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-6695     TCGA-06-6697     TCGA-06-6698     TCGA-06-6699 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-6700     TCGA-06-6701     TCGA-12-5295     TCGA-12-5299 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-12-5301     TCGA-14-0740     TCGA-14-0781     TCGA-14-0862 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-14-1043     TCGA-14-1395     TCGA-14-1450     TCGA-15-1444 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-19-5947     TCGA-19-5950     TCGA-19-5951     TCGA-19-5952 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-19-5953     TCGA-19-5954     TCGA-19-5955     TCGA-19-5958 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-19-5959     TCGA-19-5960     TCGA-26-1442     TCGA-26-5132 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-26-5133     TCGA-26-5134     TCGA-26-5135     TCGA-26-5136 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-26-5139     TCGA-26-6173     TCGA-26-6174     TCGA-28-2501 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-2510     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5211     TCGA-28-5213     TCGA-28-5214 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-5215     TCGA-28-5216     TCGA-28-5218     TCGA-28-5219 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-5220     TCGA-28-6450     TCGA-32-1979     TCGA-32-1980 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-32-5222     TCGA-41-5651     TCGA-41-6646     TCGA-74-6573 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-74-6575     TCGA-74-6577     TCGA-74-6578     TCGA-74-6584 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-4925     TCGA-76-4926     TCGA-76-4927     TCGA-76-4929 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-4934     TCGA-76-4935 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6191     TCGA-76-6192     TCGA-76-6193     TCGA-76-6280 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6283     TCGA-76-6285     TCGA-76-6286 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6656     TCGA-76-6657     TCGA-76-6660     TCGA-76-6661 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6662     TCGA-76-6663     TCGA-76-6664     TCGA-81-5910 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-81-5911     TCGA-87-5896 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  BRAF MUTATED        1      1      0      1
  BRAF WILD-TYPE     40     37     31     32
D14V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             40
  CLUS_2            1             37
  CLUS_3            0             31
  CLUS_4            1             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
  BRAF MUTATED        2      1      0
  BRAF WILD-TYPE     46     51     43
D14V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             46
  CLUS_2            1             51
  CLUS_3            0             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      2      0
  BRAF WILD-TYPE     43     60     35
D14V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             43
  CLUS_2            2             60
  CLUS_3            0             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  BRAF MUTATED        1      2      0
  BRAF WILD-TYPE     30     84     24
D14V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             30
  CLUS_2            2             84
  CLUS_3            0             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = EGFR MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED       20      7     31     10
  EGFR WILD-TYPE     49     36     43     44
D15V1, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           20             49
  CLUS_2            7             36
  CLUS_3           31             43
  CLUS_4           10             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED       18      7     17     26
  EGFR WILD-TYPE     45     43     31     53
D15V2, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           18             45
  CLUS_2            7             43
  CLUS_3           17             31
  CLUS_4           26             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED       22     27      8     17
  EGFR WILD-TYPE     55     66     37     43
D15V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           22             55
  CLUS_2           27             66
  CLUS_3            8             37
  CLUS_4           17             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED       30     19     25
  EGFR WILD-TYPE    108     42     51
D15V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           30            108
  CLUS_2           19             42
  CLUS_3           25             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED       17     46      9
  EGFR WILD-TYPE     68     61     72
D15V5, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           17             68
  CLUS_2           46             61
  CLUS_3            9             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
  EGFR MUTATED        6     14      1
  EGFR WILD-TYPE     29     30     28
D15V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            6             29
  CLUS_2           14             30
  CLUS_3            1             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  EGFR MUTATED       13      5     16      2
  EGFR WILD-TYPE     28     33     15     31
D15V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           13             28
  CLUS_2            5             33
  CLUS_3           16             15
  CLUS_4            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table 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        8      7     21
  EGFR WILD-TYPE     40     45     22
D15V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            8             40
  CLUS_2            7             45
  CLUS_3           21             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        8     22     15
  EGFR WILD-TYPE     36     40     20
D15V9, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            8             36
  CLUS_2           22             40
  CLUS_3           15             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  EGFR MUTATED        3     32     10
  EGFR WILD-TYPE     28     54     14
D15V10, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            3             28
  CLUS_2           32             54
  CLUS_3           10             14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = PDGFRA MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDGFRA MUTATED        1      6      2      1
  PDGFRA WILD-TYPE     68     37     72     53
D16V1, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              1               68
  CLUS_2              6               37
  CLUS_3              2               72
  CLUS_4              1               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDGFRA MUTATED        1      5      2      2
  PDGFRA WILD-TYPE     62     45     46     77
D16V2, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              1               62
  CLUS_2              5               45
  CLUS_3              2               46
  CLUS_4              2               77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDGFRA MUTATED        4      3      2      2
  PDGFRA WILD-TYPE     73     90     43     58
D16V3, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              4               73
  CLUS_2              3               90
  CLUS_3              2               43
  CLUS_4              2               58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PDGFRA MUTATED        9      1      1
  PDGFRA WILD-TYPE    129     60     75
D16V4, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              9              129
  CLUS_2              1               60
  CLUS_3              1               75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PDGFRA MUTATED        3      3      5
  PDGFRA WILD-TYPE     82    104     76
D16V5, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              3               82
  CLUS_2              3              104
  CLUS_3              5               76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PDGFRA MUTATED        0      0      2
  PDGFRA WILD-TYPE     35     44     27
D16V6, multiclass
[1] "Remove cluster labels:" "PDGFRA MUTATED"        
clus
  PDGFRA MUTATED PDGFRA WILD-TYPE 
               2              106 
      TCGA-06-0650       TCGA-06-1804       TCGA-06-1806       TCGA-06-5408 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6388 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-06-6389       TCGA-06-6390       TCGA-06-6391       TCGA-06-6693 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-06-6694       TCGA-06-6695       TCGA-06-6697       TCGA-06-6698 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-06-6699       TCGA-06-6700       TCGA-06-6701       TCGA-12-5295 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-12-5299       TCGA-12-5301       TCGA-14-0781       TCGA-14-0862 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-14-1043       TCGA-14-1395       TCGA-14-1450       TCGA-15-1444 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-19-5947       TCGA-19-5950       TCGA-19-5951       TCGA-19-5952 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-19-5953       TCGA-19-5954       TCGA-19-5955       TCGA-19-5958 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-19-5959       TCGA-19-5960       TCGA-26-1442       TCGA-26-5132 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-26-5133       TCGA-26-5135       TCGA-26-5136       TCGA-26-5139 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-26-6173       TCGA-26-6174       TCGA-28-2501       TCGA-28-2510 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-28-5204       TCGA-28-5207       TCGA-28-5208       TCGA-28-5209 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-28-5211       TCGA-28-5213       TCGA-28-5214       TCGA-28-5215 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-28-5216       TCGA-28-5218       TCGA-28-5219       TCGA-28-5220 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-28-6450       TCGA-32-1979       TCGA-32-1980       TCGA-32-5222 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-41-5651       TCGA-41-6646       TCGA-74-6573       TCGA-74-6575 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-74-6577       TCGA-74-6578       TCGA-74-6584       TCGA-76-4925 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-76-4926       TCGA-76-4927       TCGA-76-4928       TCGA-76-4929 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-76-4931       TCGA-76-4932       TCGA-76-4934       TCGA-76-4935 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-76-6191       TCGA-76-6192       TCGA-76-6193       TCGA-76-6280 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-76-6282       TCGA-76-6283       TCGA-76-6285       TCGA-76-6286 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-76-6656       TCGA-76-6657       TCGA-76-6660       TCGA-76-6661 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-76-6662       TCGA-76-6663       TCGA-76-6664       TCGA-81-5910 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
      TCGA-81-5911       TCGA-87-5896 
"PDGFRA WILD-TYPE" "PDGFRA WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PDGFRA MUTATED        2      1      1      1
  PDGFRA WILD-TYPE     39     37     30     32
D16V7, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              2               39
  CLUS_2              1               37
  CLUS_3              1               30
  CLUS_4              1               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
  PDGFRA MUTATED        2      2      1
  PDGFRA WILD-TYPE     46     50     42
D16V8, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              2               46
  CLUS_2              2               50
  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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PDGFRA MUTATED        5      1      0
  PDGFRA WILD-TYPE     39     61     35
D16V9, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              5               39
  CLUS_2              1               61
  CLUS_3              0               35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  PDGFRA MUTATED        5      1      0
  PDGFRA WILD-TYPE     26     85     24
D16V10, multiclass
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  CLUS_1              5               26
  CLUS_2              1               85
  CLUS_3              0               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = KDR MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        1      2      1      4
  KDR WILD-TYPE     68     41     73     50
D17V1, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1            68
  CLUS_2           2            41
  CLUS_3           1            73
  CLUS_4           4            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        1      3      1      3
  KDR WILD-TYPE     62     47     47     76
D17V2, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1            62
  CLUS_2           3            47
  CLUS_3           1            47
  CLUS_4           3            76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        2      1      3      2
  KDR WILD-TYPE     75     92     42     58
D17V3, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           2            75
  CLUS_2           1            92
  CLUS_3           3            42
  CLUS_4           2            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        6      1      1
  KDR WILD-TYPE    132     60     75
D17V4, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           6           132
  CLUS_2           1            60
  CLUS_3           1            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        2      2      4
  KDR WILD-TYPE     83    105     77
D17V5, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           2            83
  CLUS_2           2           105
  CLUS_3           4            77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        1      1      1
  KDR WILD-TYPE     34     43     28
D17V6, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           1            34
  CLUS_2           1            43
  CLUS_3           1            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KDR MUTATED        3      0      0      2
  KDR WILD-TYPE     38     38     31     31
D17V7, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           3            38
  CLUS_2           0            38
  CLUS_3           0            31
  CLUS_4           2            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        3      1      1
  KDR WILD-TYPE     45     51     42
D17V8, multiclass
        clus
vv       KDR MUTATED KDR WILD-TYPE
  CLUS_1           3            45
  CLUS_2           1            51
  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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        0      0      1
  KDR WILD-TYPE     44     62     34
D17V9, multiclass
[1] "Remove cluster labels:" "KDR MUTATED"           
clus
  KDR MUTATED KDR WILD-TYPE 
            1           140 
   TCGA-02-0047    TCGA-02-0055    TCGA-02-2483    TCGA-02-2485    TCGA-02-2486 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0129    TCGA-06-0130    TCGA-06-0132    TCGA-06-0141    TCGA-06-0157 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0158    TCGA-06-0168    TCGA-06-0174    TCGA-06-0178    TCGA-06-0184 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0219    TCGA-06-0238    TCGA-06-0644    TCGA-06-0645    TCGA-06-0646 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0649    TCGA-06-0686    TCGA-06-0743    TCGA-06-0744    TCGA-06-0745 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0747    TCGA-06-0749    TCGA-06-0750    TCGA-06-0878    TCGA-06-1804 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-2557    TCGA-06-2558    TCGA-06-2559    TCGA-06-2561    TCGA-06-2562 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-2563    TCGA-06-2564    TCGA-06-2565    TCGA-06-2567    TCGA-06-2569 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-2570    TCGA-06-5408    TCGA-06-5410    TCGA-06-5411    TCGA-06-5412 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-5413    TCGA-06-5414    TCGA-06-5415    TCGA-06-5417    TCGA-06-5418 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-5856    TCGA-06-5858    TCGA-06-5859    TCGA-08-0386    TCGA-12-0616 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-12-0618    TCGA-12-0619    TCGA-12-0821    TCGA-12-1597    TCGA-12-3650 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-12-3652    TCGA-12-3653    TCGA-12-5295    TCGA-12-5299    TCGA-14-0781 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-14-0787    TCGA-14-0789    TCGA-14-0790    TCGA-14-0817    TCGA-14-1823 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-14-1825    TCGA-14-1829    TCGA-14-2554    TCGA-15-0742    TCGA-15-1444 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-16-0846    TCGA-16-1045    TCGA-19-1390    TCGA-19-2619    TCGA-19-2620 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-19-2624    TCGA-19-2625    TCGA-19-2629    TCGA-19-5960    TCGA-26-1442 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-26-5132    TCGA-26-5133    TCGA-26-5134    TCGA-26-5135    TCGA-26-5136 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-26-5139    TCGA-27-1830    TCGA-27-1831    TCGA-27-1832    TCGA-27-1834 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-27-1835    TCGA-27-1837    TCGA-27-2519    TCGA-27-2521    TCGA-27-2523 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-27-2524    TCGA-27-2526    TCGA-27-2528    TCGA-28-1747    TCGA-28-1753 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-28-2499    TCGA-28-2509    TCGA-28-2510    TCGA-28-2513    TCGA-28-2514 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-28-5204    TCGA-28-5207    TCGA-28-5208    TCGA-28-5209    TCGA-28-5213 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-28-5215    TCGA-28-5216    TCGA-28-5218    TCGA-28-5220    TCGA-32-1970 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-32-1980    TCGA-32-1982    TCGA-32-2615    TCGA-32-2632    TCGA-32-2634 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-32-2638    TCGA-32-4213    TCGA-32-5222    TCGA-41-2571    TCGA-41-2572 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-41-3915    TCGA-41-4097    TCGA-41-5651    TCGA-76-4925    TCGA-76-4926 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-76-4927    TCGA-76-4928    TCGA-76-4929    TCGA-76-4931    TCGA-76-4932 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  KDR MUTATED        0      0      1
  KDR WILD-TYPE     31     86     23
D17V10, multiclass
[1] "Remove cluster labels:" "KDR MUTATED"           
clus
  KDR MUTATED KDR WILD-TYPE 
            1           140 
   TCGA-02-0047    TCGA-02-0055    TCGA-02-2483    TCGA-02-2485    TCGA-02-2486 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0129    TCGA-06-0130    TCGA-06-0132    TCGA-06-0141    TCGA-06-0157 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0158    TCGA-06-0168    TCGA-06-0174    TCGA-06-0178    TCGA-06-0184 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0219    TCGA-06-0238    TCGA-06-0644    TCGA-06-0645    TCGA-06-0646 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0649    TCGA-06-0686    TCGA-06-0743    TCGA-06-0744    TCGA-06-0745 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-0747    TCGA-06-0749    TCGA-06-0750    TCGA-06-0878    TCGA-06-1804 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-2557    TCGA-06-2558    TCGA-06-2559    TCGA-06-2561    TCGA-06-2562 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-2563    TCGA-06-2564    TCGA-06-2565    TCGA-06-2567    TCGA-06-2569 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-2570    TCGA-06-5408    TCGA-06-5410    TCGA-06-5411    TCGA-06-5412 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-5413    TCGA-06-5414    TCGA-06-5415    TCGA-06-5417    TCGA-06-5418 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-06-5856    TCGA-06-5858    TCGA-06-5859    TCGA-08-0386    TCGA-12-0616 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-12-0618    TCGA-12-0619    TCGA-12-0821    TCGA-12-1597    TCGA-12-3650 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-12-3652    TCGA-12-3653    TCGA-12-5295    TCGA-12-5299    TCGA-14-0781 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-14-0787    TCGA-14-0789    TCGA-14-0790    TCGA-14-0817    TCGA-14-1823 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-14-1825    TCGA-14-1829    TCGA-14-2554    TCGA-15-0742    TCGA-15-1444 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-16-0846    TCGA-16-1045    TCGA-19-1390    TCGA-19-2619    TCGA-19-2620 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-19-2624    TCGA-19-2625    TCGA-19-2629    TCGA-19-5960    TCGA-26-1442 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-26-5132    TCGA-26-5133    TCGA-26-5134    TCGA-26-5135    TCGA-26-5136 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-26-5139    TCGA-27-1830    TCGA-27-1831    TCGA-27-1832    TCGA-27-1834 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-27-1835    TCGA-27-1837    TCGA-27-2519    TCGA-27-2521    TCGA-27-2523 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-27-2524    TCGA-27-2526    TCGA-27-2528    TCGA-28-1747    TCGA-28-1753 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-28-2499    TCGA-28-2509    TCGA-28-2510    TCGA-28-2513    TCGA-28-2514 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-28-5204    TCGA-28-5207    TCGA-28-5208    TCGA-28-5209    TCGA-28-5213 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-28-5215    TCGA-28-5216    TCGA-28-5218    TCGA-28-5220    TCGA-32-1970 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-32-1980    TCGA-32-1982    TCGA-32-2615    TCGA-32-2632    TCGA-32-2634 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-32-2638    TCGA-32-4213    TCGA-32-5222    TCGA-41-2571    TCGA-41-2572 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-41-3915    TCGA-41-4097    TCGA-41-5651    TCGA-76-4925    TCGA-76-4926 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 
   TCGA-76-4927    TCGA-76-4928    TCGA-76-4929    TCGA-76-4931    TCGA-76-4932 
"KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" "KDR WILD-TYPE" 

Clustering(18) Variable = TMPRSS6 MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMPRSS6 MUTATED        2      0      3      1
  TMPRSS6 WILD-TYPE     67     43     71     53
D18V1, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               2                67
  CLUS_2               0                43
  CLUS_3               3                71
  CLUS_4               1                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMPRSS6 MUTATED        3      1      1      1
  TMPRSS6 WILD-TYPE     60     49     47     78
D18V2, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               3                60
  CLUS_2               1                49
  CLUS_3               1                47
  CLUS_4               1                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMPRSS6 MUTATED        3      1      1      1
  TMPRSS6 WILD-TYPE     74     92     44     59
D18V3, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               3                74
  CLUS_2               1                92
  CLUS_3               1                44
  CLUS_4               1                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMPRSS6 MUTATED        2      3      1
  TMPRSS6 WILD-TYPE    136     58     75
D18V4, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               2               136
  CLUS_2               3                58
  CLUS_3               1                75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMPRSS6 MUTATED        1      3      2
  TMPRSS6 WILD-TYPE     84    104     79
D18V5, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               1                84
  CLUS_2               3               104
  CLUS_3               2                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMPRSS6 MUTATED        1      2      0
  TMPRSS6 WILD-TYPE     34     42     29
D18V6, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               1                34
  CLUS_2               2                42
  CLUS_3               0                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TMPRSS6 MUTATED        2      0      2      0
  TMPRSS6 WILD-TYPE     39     38     29     33
D18V7, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               2                39
  CLUS_2               0                38
  CLUS_3               2                29
  CLUS_4               0                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
  TMPRSS6 MUTATED        2      0      2
  TMPRSS6 WILD-TYPE     46     52     41
D18V8, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               2                46
  CLUS_2               0                52
  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"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMPRSS6 MUTATED        1      4      1
  TMPRSS6 WILD-TYPE     43     58     34
D18V9, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               1                43
  CLUS_2               4                58
  CLUS_3               1                34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  TMPRSS6 MUTATED        1      4      1
  TMPRSS6 WILD-TYPE     30     82     23
D18V10, multiclass
        clus
vv       TMPRSS6 MUTATED TMPRSS6 WILD-TYPE
  CLUS_1               1                30
  CLUS_2               4                82
  CLUS_3               1                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = CHD8 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHD8 MUTATED        3      2      1      2
  CHD8 WILD-TYPE     66     41     73     52
D19V1, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            3             66
  CLUS_2            2             41
  CLUS_3            1             73
  CLUS_4            2             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHD8 MUTATED        2      2      0      4
  CHD8 WILD-TYPE     61     48     48     75
D19V2, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            2             61
  CLUS_2            2             48
  CLUS_3            0             48
  CLUS_4            4             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHD8 MUTATED        0      3      3      2
  CHD8 WILD-TYPE     77     90     42     58
D19V3, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            0             77
  CLUS_2            3             90
  CLUS_3            3             42
  CLUS_4            2             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CHD8 MUTATED        5      2      1
  CHD8 WILD-TYPE    133     59     75
D19V4, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            5            133
  CLUS_2            2             59
  CLUS_3            1             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CHD8 MUTATED        1      3      5
  CHD8 WILD-TYPE     84    104     76
D19V5, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            1             84
  CLUS_2            3            104
  CLUS_3            5             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CHD8 MUTATED        2      3      2
  CHD8 WILD-TYPE     33     41     27
D19V6, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            2             33
  CLUS_2            3             41
  CLUS_3            2             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CHD8 MUTATED        2      4      2      1
  CHD8 WILD-TYPE     39     34     29     32
D19V7, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            2             39
  CLUS_2            4             34
  CLUS_3            2             29
  CLUS_4            1             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
  CHD8 MUTATED        2      4      3
  CHD8 WILD-TYPE     46     48     40
D19V8, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            2             46
  CLUS_2            4             48
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CHD8 MUTATED        2      1      3
  CHD8 WILD-TYPE     42     61     32
D19V9, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            2             42
  CLUS_2            1             61
  CLUS_3            3             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CHD8 MUTATED        2      4      0
  CHD8 WILD-TYPE     29     82     24
D19V10, multiclass
        clus
vv       CHD8 MUTATED CHD8 WILD-TYPE
  CLUS_1            2             29
  CLUS_2            4             82
  CLUS_3            0             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = SEMA3C MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA3C MUTATED        3      4      2      2
  SEMA3C WILD-TYPE     66     39     72     52
D20V1, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              3               66
  CLUS_2              4               39
  CLUS_3              2               72
  CLUS_4              2               52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA3C MUTATED        1      5      1      4
  SEMA3C WILD-TYPE     62     45     47     75
D20V2, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              1               62
  CLUS_2              5               45
  CLUS_3              1               47
  CLUS_4              4               75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA3C MUTATED        3      7      1      0
  SEMA3C WILD-TYPE     74     86     44     60
D20V3, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              3               74
  CLUS_2              7               86
  CLUS_3              1               44
  CLUS_4              0               60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA3C MUTATED        5      2      4
  SEMA3C WILD-TYPE    133     59     72
D20V4, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              5              133
  CLUS_2              2               59
  CLUS_3              4               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
  SEMA3C MUTATED        5      4      2
  SEMA3C WILD-TYPE     80    103     79
D20V5, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              5               80
  CLUS_2              4              103
  CLUS_3              2               79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA3C MUTATED        0      1      0
  SEMA3C WILD-TYPE     35     43     29
D20V6, multiclass
[1] "Remove cluster labels:" "SEMA3C MUTATED"        
clus
  SEMA3C MUTATED SEMA3C WILD-TYPE 
               1              107 
      TCGA-06-0650       TCGA-06-1804       TCGA-06-1806       TCGA-06-5408 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6388 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-06-6389       TCGA-06-6390       TCGA-06-6391       TCGA-06-6693 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-06-6694       TCGA-06-6695       TCGA-06-6697       TCGA-06-6698 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-06-6699       TCGA-06-6700       TCGA-06-6701       TCGA-12-5295 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-12-5299       TCGA-12-5301       TCGA-14-0740       TCGA-14-0781 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-14-0862       TCGA-14-1043       TCGA-14-1395       TCGA-14-1450 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-15-1444       TCGA-19-5947       TCGA-19-5950       TCGA-19-5951 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-19-5952       TCGA-19-5953       TCGA-19-5954       TCGA-19-5955 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-19-5958       TCGA-19-5959       TCGA-19-5960       TCGA-26-1442 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-26-5132       TCGA-26-5133       TCGA-26-5134       TCGA-26-5135 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-26-5136       TCGA-26-5139       TCGA-26-6173       TCGA-26-6174 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-28-2501       TCGA-28-2510       TCGA-28-5204       TCGA-28-5207 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-28-5208       TCGA-28-5209       TCGA-28-5211       TCGA-28-5213 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-28-5214       TCGA-28-5215       TCGA-28-5216       TCGA-28-5218 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-28-5219       TCGA-28-5220       TCGA-28-6450       TCGA-32-1979 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-32-1980       TCGA-41-5651       TCGA-41-6646       TCGA-74-6573 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-74-6575       TCGA-74-6577       TCGA-74-6578       TCGA-74-6584 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-76-4925       TCGA-76-4926       TCGA-76-4927       TCGA-76-4928 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-76-4929       TCGA-76-4931       TCGA-76-4932       TCGA-76-4934 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-76-4935       TCGA-76-6191       TCGA-76-6192       TCGA-76-6193 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-76-6280       TCGA-76-6282       TCGA-76-6283       TCGA-76-6285 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-76-6286       TCGA-76-6656       TCGA-76-6657       TCGA-76-6660 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-76-6661       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
      TCGA-81-5910       TCGA-81-5911       TCGA-87-5896 
"SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" "SEMA3C WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SEMA3C MUTATED        2      2      0      0
  SEMA3C WILD-TYPE     39     36     31     33
D20V7, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              2               39
  CLUS_2              2               36
  CLUS_3              0               31
  CLUS_4              0               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
  SEMA3C MUTATED        1      1      2
  SEMA3C WILD-TYPE     47     51     41
D20V8, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              1               47
  CLUS_2              1               51
  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"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA3C MUTATED        6      2      1
  SEMA3C WILD-TYPE     38     60     34
D20V9, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              6               38
  CLUS_2              2               60
  CLUS_3              1               34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  SEMA3C MUTATED        4      5      0
  SEMA3C WILD-TYPE     27     81     24
D20V10, multiclass
        clus
vv       SEMA3C MUTATED SEMA3C WILD-TYPE
  CLUS_1              4               27
  CLUS_2              5               81
  CLUS_3              0               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = ZDHHC4 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZDHHC4 MUTATED        0      1      0      0
  ZDHHC4 WILD-TYPE     69     42     74     54
D21V1, multiclass
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               1              239 
      TCGA-02-0003       TCGA-02-0033       TCGA-02-0047       TCGA-02-2470 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-02-2483       TCGA-02-2485       TCGA-02-2486       TCGA-06-0122 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0124       TCGA-06-0126       TCGA-06-0128       TCGA-06-0129 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0130       TCGA-06-0132       TCGA-06-0137       TCGA-06-0139 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0140       TCGA-06-0141       TCGA-06-0142       TCGA-06-0145 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0152       TCGA-06-0154       TCGA-06-0155       TCGA-06-0157 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0158       TCGA-06-0166       TCGA-06-0167       TCGA-06-0168 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0169       TCGA-06-0173       TCGA-06-0174       TCGA-06-0178 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0184       TCGA-06-0185       TCGA-06-0188       TCGA-06-0189 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0192       TCGA-06-0195       TCGA-06-0213       TCGA-06-0214 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0216       TCGA-06-0219       TCGA-06-0237       TCGA-06-0238 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0240       TCGA-06-0241       TCGA-06-0644       TCGA-06-0645 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0646       TCGA-06-0648       TCGA-06-0649       TCGA-06-0650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0686       TCGA-06-0743       TCGA-06-0744       TCGA-06-0745 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0747       TCGA-06-0749       TCGA-06-0750       TCGA-06-0875 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0876       TCGA-06-0877       TCGA-06-0878       TCGA-06-0879 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0881       TCGA-06-0882       TCGA-06-0939       TCGA-06-1804 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2557       TCGA-06-2558       TCGA-06-2559       TCGA-06-2561 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2569       TCGA-06-2570       TCGA-06-5408 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6389 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6390       TCGA-06-6391       TCGA-08-0386       TCGA-12-0616 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0618       TCGA-12-0619       TCGA-12-0688       TCGA-12-0692 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0821       TCGA-12-1597       TCGA-12-3649       TCGA-12-3650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5295       TCGA-12-5299 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-5301       TCGA-14-0781       TCGA-14-0786       TCGA-14-0787 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0789       TCGA-14-0790       TCGA-14-0813       TCGA-14-0817 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0871       TCGA-14-1456       TCGA-14-1823       TCGA-14-1825 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-1829       TCGA-14-2554       TCGA-14-3476       TCGA-14-4157 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-15-0742       TCGA-15-1444       TCGA-16-0846       TCGA-16-0861 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-16-1045       TCGA-16-1048       TCGA-19-1390       TCGA-19-1790 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2619       TCGA-19-2620       TCGA-19-2623       TCGA-19-2624 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2625       TCGA-19-2629       TCGA-19-2631       TCGA-19-4068 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5947       TCGA-19-5950       TCGA-19-5951       TCGA-19-5952 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5954       TCGA-19-5955       TCGA-19-5958       TCGA-19-5959 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1439       TCGA-26-1442       TCGA-26-5132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5133       TCGA-26-5134       TCGA-26-5135       TCGA-26-5136 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5139       TCGA-27-1830       TCGA-27-1831       TCGA-27-1832 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1833       TCGA-27-1834       TCGA-27-1835       TCGA-27-1836 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1837       TCGA-27-1838       TCGA-27-2518       TCGA-27-2519 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2521       TCGA-27-2523       TCGA-27-2524       TCGA-27-2526 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2527       TCGA-27-2528       TCGA-28-1747       TCGA-28-1753 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-2501       TCGA-28-2502       TCGA-28-2509       TCGA-28-2510 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-2513       TCGA-28-2514       TCGA-28-5204       TCGA-28-5207 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5208       TCGA-28-5209       TCGA-28-5213       TCGA-28-5214 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5215       TCGA-28-5216       TCGA-28-5218       TCGA-28-5219 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5220       TCGA-28-6450       TCGA-32-1970       TCGA-32-1977 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1979       TCGA-32-1980       TCGA-32-1982       TCGA-32-1986 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1991       TCGA-32-2491       TCGA-32-2494       TCGA-32-2495 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-2615       TCGA-32-2632       TCGA-32-2634       TCGA-32-2638 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-4208       TCGA-32-4209       TCGA-32-4210       TCGA-32-4211 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-4213       TCGA-32-4719       TCGA-32-5222       TCGA-41-2571 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-2572       TCGA-41-2573       TCGA-41-2575       TCGA-41-3392 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-3393       TCGA-41-3915       TCGA-41-4097       TCGA-76-4925 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4926       TCGA-76-4927       TCGA-76-4928       TCGA-76-4929 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4931       TCGA-76-4932       TCGA-76-4934       TCGA-76-4935 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6191       TCGA-76-6192       TCGA-76-6193       TCGA-76-6282 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6285       TCGA-81-5910       TCGA-87-5896 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZDHHC4 MUTATED        0      1      0      0
  ZDHHC4 WILD-TYPE     63     49     48     79
D21V2, multiclass
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               1              239 
      TCGA-02-0003       TCGA-02-0033       TCGA-02-0047       TCGA-02-2470 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-02-2483       TCGA-02-2485       TCGA-02-2486       TCGA-06-0122 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0124       TCGA-06-0126       TCGA-06-0128       TCGA-06-0129 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0130       TCGA-06-0132       TCGA-06-0137       TCGA-06-0139 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0140       TCGA-06-0141       TCGA-06-0142       TCGA-06-0145 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0152       TCGA-06-0154       TCGA-06-0155       TCGA-06-0157 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0158       TCGA-06-0166       TCGA-06-0167       TCGA-06-0168 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0169       TCGA-06-0173       TCGA-06-0174       TCGA-06-0178 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0184       TCGA-06-0185       TCGA-06-0188       TCGA-06-0189 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0192       TCGA-06-0195       TCGA-06-0213       TCGA-06-0214 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0216       TCGA-06-0219       TCGA-06-0237       TCGA-06-0238 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0240       TCGA-06-0241       TCGA-06-0644       TCGA-06-0645 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0646       TCGA-06-0648       TCGA-06-0649       TCGA-06-0650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0686       TCGA-06-0743       TCGA-06-0744       TCGA-06-0745 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0747       TCGA-06-0749       TCGA-06-0750       TCGA-06-0875 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0876       TCGA-06-0877       TCGA-06-0878       TCGA-06-0879 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0881       TCGA-06-0882       TCGA-06-0939       TCGA-06-1804 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2557       TCGA-06-2558       TCGA-06-2559       TCGA-06-2561 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2569       TCGA-06-2570       TCGA-06-5408 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6389 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6390       TCGA-06-6391       TCGA-08-0386       TCGA-12-0616 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0618       TCGA-12-0619       TCGA-12-0688       TCGA-12-0692 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0821       TCGA-12-1597       TCGA-12-3649       TCGA-12-3650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5295       TCGA-12-5299 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-5301       TCGA-14-0781       TCGA-14-0786       TCGA-14-0787 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0789       TCGA-14-0790       TCGA-14-0813       TCGA-14-0817 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0871       TCGA-14-1456       TCGA-14-1823       TCGA-14-1825 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-1829       TCGA-14-2554       TCGA-14-3476       TCGA-14-4157 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-15-0742       TCGA-15-1444       TCGA-16-0846       TCGA-16-0861 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-16-1045       TCGA-16-1048       TCGA-19-1390       TCGA-19-1790 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2619       TCGA-19-2620       TCGA-19-2623       TCGA-19-2624 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2625       TCGA-19-2629       TCGA-19-2631       TCGA-19-4068 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5947       TCGA-19-5950       TCGA-19-5951       TCGA-19-5952 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5954       TCGA-19-5955       TCGA-19-5958       TCGA-19-5959 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1439       TCGA-26-1442       TCGA-26-5132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5133       TCGA-26-5134       TCGA-26-5135       TCGA-26-5136 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5139       TCGA-27-1830       TCGA-27-1831       TCGA-27-1832 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1833       TCGA-27-1834       TCGA-27-1835       TCGA-27-1836 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1837       TCGA-27-1838       TCGA-27-2518       TCGA-27-2519 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2521       TCGA-27-2523       TCGA-27-2524       TCGA-27-2526 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2527       TCGA-27-2528       TCGA-28-1747       TCGA-28-1753 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-2501       TCGA-28-2502       TCGA-28-2509       TCGA-28-2510 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-2513       TCGA-28-2514       TCGA-28-5204       TCGA-28-5207 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5208       TCGA-28-5209       TCGA-28-5213       TCGA-28-5214 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5215       TCGA-28-5216       TCGA-28-5218       TCGA-28-5219 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5220       TCGA-28-6450       TCGA-32-1970       TCGA-32-1977 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1979       TCGA-32-1980       TCGA-32-1982       TCGA-32-1986 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1991       TCGA-32-2491       TCGA-32-2494       TCGA-32-2495 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-2615       TCGA-32-2632       TCGA-32-2634       TCGA-32-2638 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-4208       TCGA-32-4209       TCGA-32-4210       TCGA-32-4211 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-4213       TCGA-32-4719       TCGA-32-5222       TCGA-41-2571 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-2572       TCGA-41-2573       TCGA-41-2575       TCGA-41-3392 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-3393       TCGA-41-3915       TCGA-41-4097       TCGA-76-4925 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4926       TCGA-76-4927       TCGA-76-4928       TCGA-76-4929 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4931       TCGA-76-4932       TCGA-76-4934       TCGA-76-4935 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6191       TCGA-76-6192       TCGA-76-6193       TCGA-76-6282 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6285       TCGA-81-5910       TCGA-87-5896 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZDHHC4 MUTATED        0      3      0      0
  ZDHHC4 WILD-TYPE     77     90     45     60
D21V3, multiclass
        clus
vv       ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  CLUS_1              0               77
  CLUS_2              3               90
  CLUS_3              0               45
  CLUS_4              0               60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZDHHC4 MUTATED        2      0      1
  ZDHHC4 WILD-TYPE    136     61     75
D21V4, multiclass
        clus
vv       ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  CLUS_1              2              136
  CLUS_2              0               61
  CLUS_3              1               75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZDHHC4 MUTATED        3      0      0
  ZDHHC4 WILD-TYPE     82    107     81
D21V5, multiclass
        clus
vv       ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  CLUS_1              3               82
  CLUS_2              0              107
  CLUS_3              0               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZDHHC4 MUTATED        0      1      2
  ZDHHC4 WILD-TYPE     35     43     27
D21V6, multiclass
        clus
vv       ZDHHC4 MUTATED ZDHHC4 WILD-TYPE
  CLUS_1              0               35
  CLUS_2              1               43
  CLUS_3              2               27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  ZDHHC4 MUTATED        0      1      0      1
  ZDHHC4 WILD-TYPE     41     37     31     32
D21V7, multiclass
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               2              141 
      TCGA-02-0003       TCGA-02-2470       TCGA-02-2485       TCGA-06-0126 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0128       TCGA-06-0129       TCGA-06-0130       TCGA-06-0154 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0155       TCGA-06-0189       TCGA-06-0238       TCGA-06-0644 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0650       TCGA-06-0875       TCGA-06-0876       TCGA-06-0877 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0879       TCGA-06-0882       TCGA-06-0939 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-1804       TCGA-06-1806       TCGA-06-2557       TCGA-06-2558 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2559       TCGA-06-2562       TCGA-06-2563       TCGA-06-2564 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2565       TCGA-06-2567       TCGA-06-2570       TCGA-06-5408 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6388 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6389       TCGA-06-6390       TCGA-06-6391       TCGA-06-6693 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6694       TCGA-06-6695       TCGA-06-6697       TCGA-06-6698 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6699       TCGA-06-6700       TCGA-06-6701       TCGA-08-0386 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0692       TCGA-12-1597       TCGA-12-3649       TCGA-12-3650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5295       TCGA-12-5301 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0813       TCGA-14-0862       TCGA-14-0871       TCGA-14-1823 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-16-0846       TCGA-19-1390       TCGA-19-1790       TCGA-19-2619 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2620       TCGA-19-2625       TCGA-19-2631       TCGA-19-4068 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5947       TCGA-19-5950       TCGA-19-5951       TCGA-19-5952 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5953       TCGA-19-5954       TCGA-19-5955       TCGA-19-5958 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5959       TCGA-19-5960       TCGA-26-1442       TCGA-26-5132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5133       TCGA-26-5134       TCGA-26-6173       TCGA-26-6174 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1830       TCGA-27-1831       TCGA-27-1832       TCGA-27-1833 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1834       TCGA-27-1836       TCGA-27-2518       TCGA-27-2528 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-1747       TCGA-28-1753       TCGA-28-2501       TCGA-28-5208 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5214       TCGA-32-1970       TCGA-32-1982       TCGA-32-1986 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1991       TCGA-32-4210       TCGA-32-4211       TCGA-32-5222 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-2573       TCGA-41-2575       TCGA-41-3392       TCGA-41-3393 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-3915       TCGA-41-4097       TCGA-41-6646       TCGA-74-6573 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-74-6575       TCGA-74-6577       TCGA-74-6578       TCGA-74-6584 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4926       TCGA-76-4927       TCGA-76-4928       TCGA-76-4929 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4931       TCGA-76-4932       TCGA-76-6192       TCGA-76-6193 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6282       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6660       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-81-5910 
"ZDHHC4 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZDHHC4 MUTATED        1      1      0
  ZDHHC4 WILD-TYPE     47     51     43
D21V8, multiclass
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               2              141 
      TCGA-02-0003       TCGA-02-2470       TCGA-02-2485       TCGA-06-0126 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0128       TCGA-06-0129       TCGA-06-0130       TCGA-06-0154 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0155       TCGA-06-0189       TCGA-06-0238       TCGA-06-0644 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0650       TCGA-06-0875       TCGA-06-0876       TCGA-06-0877 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0879       TCGA-06-0882       TCGA-06-0939 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-1804       TCGA-06-1806       TCGA-06-2557       TCGA-06-2558 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2559       TCGA-06-2562       TCGA-06-2563       TCGA-06-2564 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2565       TCGA-06-2567       TCGA-06-2570       TCGA-06-5408 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5414       TCGA-06-5415       TCGA-06-5417       TCGA-06-5418 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5856       TCGA-06-5858       TCGA-06-5859       TCGA-06-6388 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6389       TCGA-06-6390       TCGA-06-6391       TCGA-06-6693 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6694       TCGA-06-6695       TCGA-06-6697       TCGA-06-6698 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-6699       TCGA-06-6700       TCGA-06-6701       TCGA-08-0386 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0692       TCGA-12-1597       TCGA-12-3649       TCGA-12-3650 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5295       TCGA-12-5301 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0813       TCGA-14-0862       TCGA-14-0871       TCGA-14-1823 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-16-0846       TCGA-19-1390       TCGA-19-1790       TCGA-19-2619 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2620       TCGA-19-2625       TCGA-19-2631       TCGA-19-4068 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5947       TCGA-19-5950       TCGA-19-5951       TCGA-19-5952 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5953       TCGA-19-5954       TCGA-19-5955       TCGA-19-5958 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5959       TCGA-19-5960       TCGA-26-1442       TCGA-26-5132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5133       TCGA-26-5134       TCGA-26-6173       TCGA-26-6174 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1830       TCGA-27-1831       TCGA-27-1832       TCGA-27-1833 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1834       TCGA-27-1836       TCGA-27-2518       TCGA-27-2528 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-1747       TCGA-28-1753       TCGA-28-2501       TCGA-28-5208 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5214       TCGA-32-1970       TCGA-32-1982       TCGA-32-1986 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1991       TCGA-32-4210       TCGA-32-4211       TCGA-32-5222 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-2573       TCGA-41-2575       TCGA-41-3392       TCGA-41-3393 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-3915       TCGA-41-4097       TCGA-41-6646       TCGA-74-6573 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-74-6575       TCGA-74-6577       TCGA-74-6578       TCGA-74-6584 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4926       TCGA-76-4927       TCGA-76-4928       TCGA-76-4929 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4931       TCGA-76-4932       TCGA-76-6192       TCGA-76-6193 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6282       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-6660       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-81-5910 
"ZDHHC4 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZDHHC4 MUTATED        1      0      0
  ZDHHC4 WILD-TYPE     43     62     35
D21V9, multiclass
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               1              140 
      TCGA-02-0047       TCGA-02-0055       TCGA-02-2483       TCGA-02-2485 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-02-2486       TCGA-06-0129       TCGA-06-0130       TCGA-06-0132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0141       TCGA-06-0157       TCGA-06-0158       TCGA-06-0168 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0174       TCGA-06-0178       TCGA-06-0184       TCGA-06-0219 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0238       TCGA-06-0644       TCGA-06-0645       TCGA-06-0646 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0649       TCGA-06-0686       TCGA-06-0743       TCGA-06-0744 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0745       TCGA-06-0747       TCGA-06-0749       TCGA-06-0750 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0882       TCGA-06-1804       TCGA-06-2557 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2558       TCGA-06-2559       TCGA-06-2561       TCGA-06-2562 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2563       TCGA-06-2564       TCGA-06-2565       TCGA-06-2567 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2569       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5414 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5415       TCGA-06-5417       TCGA-06-5418       TCGA-06-5856 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5858       TCGA-06-5859       TCGA-08-0386       TCGA-12-0616 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0618       TCGA-12-0619       TCGA-12-0821       TCGA-12-1597 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3650       TCGA-12-3652       TCGA-12-3653       TCGA-12-5295 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-5299       TCGA-14-0781       TCGA-14-0787       TCGA-14-0789 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0790       TCGA-14-0817       TCGA-14-1823       TCGA-14-1825 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-1829       TCGA-14-2554       TCGA-15-0742       TCGA-15-1444 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-16-0846       TCGA-16-1045       TCGA-19-1390       TCGA-19-2619 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2620       TCGA-19-2624       TCGA-19-2625       TCGA-19-2629 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1442       TCGA-26-5132       TCGA-26-5133 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5134       TCGA-26-5135       TCGA-26-5136       TCGA-26-5139 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1830       TCGA-27-1831       TCGA-27-1832       TCGA-27-1834 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1835       TCGA-27-1837       TCGA-27-2519       TCGA-27-2521 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2523       TCGA-27-2524       TCGA-27-2526       TCGA-27-2528 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-1747       TCGA-28-1753       TCGA-28-2499       TCGA-28-2509 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-2510       TCGA-28-2513       TCGA-28-2514       TCGA-28-5204 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5207       TCGA-28-5208       TCGA-28-5209       TCGA-28-5213 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5215       TCGA-28-5216       TCGA-28-5218       TCGA-28-5220 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1970       TCGA-32-1980       TCGA-32-1982       TCGA-32-2615 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-2632       TCGA-32-2634       TCGA-32-2638       TCGA-32-4213 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-5222       TCGA-41-2571       TCGA-41-2572       TCGA-41-3915 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-4097       TCGA-76-4925       TCGA-76-4926       TCGA-76-4927 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4928       TCGA-76-4929       TCGA-76-4931       TCGA-76-4932 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  ZDHHC4 MUTATED        1      0      0
  ZDHHC4 WILD-TYPE     30     86     24
D21V10, multiclass
[1] "Remove cluster labels:" "ZDHHC4 MUTATED"        
clus
  ZDHHC4 MUTATED ZDHHC4 WILD-TYPE 
               1              140 
      TCGA-02-0047       TCGA-02-0055       TCGA-02-2483       TCGA-02-2485 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-02-2486       TCGA-06-0129       TCGA-06-0130       TCGA-06-0132 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0141       TCGA-06-0157       TCGA-06-0158       TCGA-06-0168 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0174       TCGA-06-0178       TCGA-06-0184       TCGA-06-0219 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0238       TCGA-06-0644       TCGA-06-0645       TCGA-06-0646 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0649       TCGA-06-0686       TCGA-06-0743       TCGA-06-0744 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0745       TCGA-06-0747       TCGA-06-0749       TCGA-06-0750 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0882       TCGA-06-1804       TCGA-06-2557 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2558       TCGA-06-2559       TCGA-06-2561       TCGA-06-2562 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2563       TCGA-06-2564       TCGA-06-2565       TCGA-06-2567 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-2569       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5414 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5415       TCGA-06-5417       TCGA-06-5418       TCGA-06-5856 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-06-5858       TCGA-06-5859       TCGA-08-0386       TCGA-12-0616 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-0618       TCGA-12-0619       TCGA-12-0821       TCGA-12-1597 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-3650       TCGA-12-3652       TCGA-12-3653       TCGA-12-5295 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-12-5299       TCGA-14-0781       TCGA-14-0787       TCGA-14-0789 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-0790       TCGA-14-0817       TCGA-14-1823       TCGA-14-1825 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-14-1829       TCGA-14-2554       TCGA-15-0742       TCGA-15-1444 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-16-0846       TCGA-16-1045       TCGA-19-1390       TCGA-19-2619 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-2620       TCGA-19-2624       TCGA-19-2625       TCGA-19-2629 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1442       TCGA-26-5132       TCGA-26-5133 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-26-5134       TCGA-26-5135       TCGA-26-5136       TCGA-26-5139 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1830       TCGA-27-1831       TCGA-27-1832       TCGA-27-1834 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-1835       TCGA-27-1837       TCGA-27-2519       TCGA-27-2521 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-27-2523       TCGA-27-2524       TCGA-27-2526       TCGA-27-2528 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-1747       TCGA-28-1753       TCGA-28-2499       TCGA-28-2509 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-2510       TCGA-28-2513       TCGA-28-2514       TCGA-28-5204 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5207       TCGA-28-5208       TCGA-28-5209       TCGA-28-5213 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-28-5215       TCGA-28-5216       TCGA-28-5218       TCGA-28-5220 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-1970       TCGA-32-1980       TCGA-32-1982       TCGA-32-2615 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-2632       TCGA-32-2634       TCGA-32-2638       TCGA-32-4213 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-32-5222       TCGA-41-2571       TCGA-41-2572       TCGA-41-3915 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-41-4097       TCGA-76-4925       TCGA-76-4926       TCGA-76-4927 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 
      TCGA-76-4928       TCGA-76-4929       TCGA-76-4931       TCGA-76-4932 
"ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" "ZDHHC4 WILD-TYPE" 

Clustering(22) Variable = MMP13 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP13 MUTATED        1      0      2      1
  MMP13 WILD-TYPE     68     43     72     53
D22V1, multiclass
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  CLUS_1             1              68
  CLUS_2             0              43
  CLUS_3             2              72
  CLUS_4             1              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP13 MUTATED        1      1      2      0
  MMP13 WILD-TYPE     62     49     46     79
D22V2, multiclass
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  CLUS_1             1              62
  CLUS_2             1              49
  CLUS_3             2              46
  CLUS_4             0              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP13 MUTATED        1      2      0      2
  MMP13 WILD-TYPE     76     91     45     58
D22V3, multiclass
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  CLUS_1             1              76
  CLUS_2             2              91
  CLUS_3             0              45
  CLUS_4             2              58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP13 MUTATED        1      0      4
  MMP13 WILD-TYPE    137     61     72
D22V4, multiclass
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  CLUS_1             1             137
  CLUS_2             0              61
  CLUS_3             4              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
  MMP13 MUTATED        0      4      1
  MMP13 WILD-TYPE     85    103     80
D22V5, multiclass
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  CLUS_1             0              85
  CLUS_2             4             103
  CLUS_3             1              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP13 MUTATED        0      2      0
  MMP13 WILD-TYPE     35     42     29
D22V6, multiclass
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2             106 
     TCGA-06-0650      TCGA-06-1804      TCGA-06-1806      TCGA-06-5408 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6700      TCGA-06-6701      TCGA-12-5295      TCGA-12-5299 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-5301      TCGA-14-0740      TCGA-14-0781      TCGA-14-0862 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-1043      TCGA-14-1395      TCGA-14-1450      TCGA-15-1444 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5947      TCGA-19-5950      TCGA-19-5951      TCGA-19-5952 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5953      TCGA-19-5954      TCGA-19-5955      TCGA-19-5958 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5959      TCGA-19-5960      TCGA-26-1442      TCGA-26-5132 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-5133      TCGA-26-5134      TCGA-26-5135      TCGA-26-5136 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-5139      TCGA-26-6173      TCGA-26-6174      TCGA-28-2501 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-2510      TCGA-28-5204      TCGA-28-5207      TCGA-28-5208 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5209      TCGA-28-5211      TCGA-28-5213      TCGA-28-5214 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5215      TCGA-28-5216      TCGA-28-5218      TCGA-28-5219 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5220      TCGA-28-6450      TCGA-32-1979      TCGA-32-1980 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-5222      TCGA-41-5651      TCGA-41-6646      TCGA-74-6573 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-74-6575      TCGA-74-6577      TCGA-74-6578      TCGA-74-6584 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4926      TCGA-76-4927      TCGA-76-4928      TCGA-76-4929 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4931      TCGA-76-4932      TCGA-76-4934      TCGA-76-4935 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6191      TCGA-76-6192      TCGA-76-6193      TCGA-76-6280 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6282      TCGA-76-6283      TCGA-76-6285      TCGA-76-6286 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6656      TCGA-76-6657      TCGA-76-6660      TCGA-76-6661 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6662      TCGA-76-6663      TCGA-76-6664      TCGA-81-5910 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-81-5911      TCGA-87-5896 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MMP13 MUTATED        0      0      2      0
  MMP13 WILD-TYPE     41     38     29     33
D22V7, multiclass
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2             141 
     TCGA-02-0003      TCGA-02-2470      TCGA-02-2485      TCGA-06-0126 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0128      TCGA-06-0129      TCGA-06-0130      TCGA-06-0154 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0155      TCGA-06-0189      TCGA-06-0238      TCGA-06-0644 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0650      TCGA-06-0875      TCGA-06-0876      TCGA-06-0877 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0879      TCGA-06-0882      TCGA-06-0939 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-1804      TCGA-06-1806      TCGA-06-2557      TCGA-06-2558 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2559      TCGA-06-2562      TCGA-06-2563      TCGA-06-2564 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2565      TCGA-06-2567      TCGA-06-2570      TCGA-06-5408 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6700      TCGA-06-6701      TCGA-08-0386      TCGA-12-0692 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-1597      TCGA-12-3649      TCGA-12-3650      TCGA-12-3653 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-5295      TCGA-12-5301      TCGA-14-0813      TCGA-14-0862 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-0871      TCGA-14-1823      TCGA-16-0846      TCGA-19-1390 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-1790      TCGA-19-2619      TCGA-19-2620      TCGA-19-2625 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-2631      TCGA-19-4068      TCGA-19-5947      TCGA-19-5950 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5951      TCGA-19-5952      TCGA-19-5953      TCGA-19-5954 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5955      TCGA-19-5958      TCGA-19-5959      TCGA-19-5960 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-1442      TCGA-26-5132      TCGA-26-5133      TCGA-26-5134 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-6173      TCGA-26-6174      TCGA-27-1830      TCGA-27-1831 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-1832      TCGA-27-1833      TCGA-27-1834      TCGA-27-1836 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-2518      TCGA-27-2528      TCGA-28-1747      TCGA-28-1753 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-2501      TCGA-28-5208      TCGA-28-5214      TCGA-32-1970 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-1982      TCGA-32-1986      TCGA-32-1991      TCGA-32-4210 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-4211      TCGA-32-5222      TCGA-41-2573      TCGA-41-2575 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-3392      TCGA-41-3393      TCGA-41-3915      TCGA-41-4097 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-5651      TCGA-41-6646      TCGA-74-6573      TCGA-74-6575 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-74-6577      TCGA-74-6578      TCGA-74-6584      TCGA-76-4926 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4927      TCGA-76-4928      TCGA-76-4929      TCGA-76-4931 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4932      TCGA-76-6192      TCGA-76-6193      TCGA-76-6282 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6283      TCGA-76-6285      TCGA-76-6656      TCGA-76-6657 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6660      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-81-5910 
"MMP13 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP13 MUTATED        0      0      2
  MMP13 WILD-TYPE     48     52     41
D22V8, multiclass
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2             141 
     TCGA-02-0003      TCGA-02-2470      TCGA-02-2485      TCGA-06-0126 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0128      TCGA-06-0129      TCGA-06-0130      TCGA-06-0154 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0155      TCGA-06-0189      TCGA-06-0238      TCGA-06-0644 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0650      TCGA-06-0875      TCGA-06-0876      TCGA-06-0877 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0879      TCGA-06-0882      TCGA-06-0939 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-1804      TCGA-06-1806      TCGA-06-2557      TCGA-06-2558 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2559      TCGA-06-2562      TCGA-06-2563      TCGA-06-2564 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2565      TCGA-06-2567      TCGA-06-2570      TCGA-06-5408 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-6700      TCGA-06-6701      TCGA-08-0386      TCGA-12-0692 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-1597      TCGA-12-3649      TCGA-12-3650      TCGA-12-3653 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-5295      TCGA-12-5301      TCGA-14-0813      TCGA-14-0862 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-0871      TCGA-14-1823      TCGA-16-0846      TCGA-19-1390 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-1790      TCGA-19-2619      TCGA-19-2620      TCGA-19-2625 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-2631      TCGA-19-4068      TCGA-19-5947      TCGA-19-5950 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5951      TCGA-19-5952      TCGA-19-5953      TCGA-19-5954 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-5955      TCGA-19-5958      TCGA-19-5959      TCGA-19-5960 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-1442      TCGA-26-5132      TCGA-26-5133      TCGA-26-5134 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-6173      TCGA-26-6174      TCGA-27-1830      TCGA-27-1831 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-1832      TCGA-27-1833      TCGA-27-1834      TCGA-27-1836 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-2518      TCGA-27-2528      TCGA-28-1747      TCGA-28-1753 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-2501      TCGA-28-5208      TCGA-28-5214      TCGA-32-1970 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-1982      TCGA-32-1986      TCGA-32-1991      TCGA-32-4210 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-4211      TCGA-32-5222      TCGA-41-2573      TCGA-41-2575 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-3392      TCGA-41-3393      TCGA-41-3915      TCGA-41-4097 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-5651      TCGA-41-6646      TCGA-74-6573      TCGA-74-6575 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-74-6577      TCGA-74-6578      TCGA-74-6584      TCGA-76-4926 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4927      TCGA-76-4928      TCGA-76-4929      TCGA-76-4931 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4932      TCGA-76-6192      TCGA-76-6193      TCGA-76-6282 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6283      TCGA-76-6285      TCGA-76-6656      TCGA-76-6657 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-6660      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-81-5910 
"MMP13 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP13 MUTATED        0      2      0
  MMP13 WILD-TYPE     44     60     35
D22V9, multiclass
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2             139 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0619      TCGA-12-0821      TCGA-12-1597 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-3650      TCGA-12-3653      TCGA-12-5295      TCGA-12-5299 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-0781      TCGA-14-0787      TCGA-14-0789      TCGA-14-0790 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-0817      TCGA-14-1823      TCGA-14-1825      TCGA-14-1829 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-2554      TCGA-15-0742      TCGA-15-1444      TCGA-16-0846 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-16-1045      TCGA-19-1390      TCGA-19-2619      TCGA-19-2620 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-2624      TCGA-19-2625      TCGA-19-2629      TCGA-19-5960 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-1442      TCGA-26-5132      TCGA-26-5133      TCGA-26-5134 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-5135      TCGA-26-5136      TCGA-26-5139      TCGA-27-1830 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1834      TCGA-27-1835 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-1837      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2528      TCGA-28-1747 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2499      TCGA-28-2509      TCGA-28-2510 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5213      TCGA-28-5215 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5216      TCGA-28-5218      TCGA-28-5220      TCGA-32-1970 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-1980      TCGA-32-1982      TCGA-32-2615      TCGA-32-2632 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-2634      TCGA-32-2638      TCGA-32-4213      TCGA-32-5222 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-2571      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4926      TCGA-76-4927      TCGA-76-4928 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4929      TCGA-76-4931      TCGA-76-4932 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MMP13 MUTATED        0      2      0
  MMP13 WILD-TYPE     31     84     24
D22V10, multiclass
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2             139 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0619      TCGA-12-0821      TCGA-12-1597 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-12-3650      TCGA-12-3653      TCGA-12-5295      TCGA-12-5299 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-0781      TCGA-14-0787      TCGA-14-0789      TCGA-14-0790 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-0817      TCGA-14-1823      TCGA-14-1825      TCGA-14-1829 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-14-2554      TCGA-15-0742      TCGA-15-1444      TCGA-16-0846 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-16-1045      TCGA-19-1390      TCGA-19-2619      TCGA-19-2620 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-19-2624      TCGA-19-2625      TCGA-19-2629      TCGA-19-5960 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-1442      TCGA-26-5132      TCGA-26-5133      TCGA-26-5134 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-26-5135      TCGA-26-5136      TCGA-26-5139      TCGA-27-1830 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1834      TCGA-27-1835 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-1837      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2528      TCGA-28-1747 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2499      TCGA-28-2509      TCGA-28-2510 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5213      TCGA-28-5215 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-28-5216      TCGA-28-5218      TCGA-28-5220      TCGA-32-1970 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-1980      TCGA-32-1982      TCGA-32-2615      TCGA-32-2632 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-32-2634      TCGA-32-2638      TCGA-32-4213      TCGA-32-5222 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-2571      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4926      TCGA-76-4927      TCGA-76-4928 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-76-4929      TCGA-76-4931      TCGA-76-4932 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 

Clustering(23) Variable = PRKCD MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKCD MUTATED        0      2      1      0
  PRKCD WILD-TYPE     69     41     73     54
D23V1, multiclass
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  CLUS_1             0              69
  CLUS_2             2              41
  CLUS_3             1              73
  CLUS_4             0              54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKCD MUTATED        0      2      1      0
  PRKCD WILD-TYPE     63     48     47     79
D23V2, multiclass
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  CLUS_1             0              63
  CLUS_2             2              48
  CLUS_3             1              47
  CLUS_4             0              79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKCD MUTATED        0      3      0      0
  PRKCD WILD-TYPE     77     90     45     60
D23V3, multiclass
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  CLUS_1             0              77
  CLUS_2             3              90
  CLUS_3             0              45
  CLUS_4             0              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRKCD MUTATED        2      0      1
  PRKCD WILD-TYPE    136     61     75
D23V4, multiclass
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  CLUS_1             2             136
  CLUS_2             0              61
  CLUS_3             1              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRKCD MUTATED        0      1      2
  PRKCD WILD-TYPE     85    106     79
D23V5, multiclass
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  CLUS_1             0              85
  CLUS_2             1             106
  CLUS_3             2              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRKCD MUTATED        0      0      1
  PRKCD WILD-TYPE     35     44     28
D23V6, multiclass
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             107 
     TCGA-06-0650      TCGA-06-1804      TCGA-06-1806      TCGA-06-5408 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6699      TCGA-06-6700      TCGA-06-6701      TCGA-12-5295 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-5299      TCGA-12-5301      TCGA-14-0740      TCGA-14-0781 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0862      TCGA-14-1043      TCGA-14-1395      TCGA-14-1450 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-15-1444      TCGA-19-5947      TCGA-19-5950      TCGA-19-5951 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5952      TCGA-19-5953      TCGA-19-5954      TCGA-19-5955 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5958      TCGA-19-5959      TCGA-19-5960      TCGA-26-1442 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5132      TCGA-26-5134      TCGA-26-5135      TCGA-26-5136 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5139      TCGA-26-6173      TCGA-26-6174      TCGA-28-2501 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-2510      TCGA-28-5204      TCGA-28-5207      TCGA-28-5208 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5209      TCGA-28-5211      TCGA-28-5213      TCGA-28-5214 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5215      TCGA-28-5216      TCGA-28-5218      TCGA-28-5219 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5220      TCGA-28-6450      TCGA-32-1979      TCGA-32-1980 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-5222      TCGA-41-5651      TCGA-41-6646      TCGA-74-6573 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-74-6575      TCGA-74-6577      TCGA-74-6578      TCGA-74-6584 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4925      TCGA-76-4926      TCGA-76-4927      TCGA-76-4928 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4929      TCGA-76-4931      TCGA-76-4932      TCGA-76-4934 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4935      TCGA-76-6191      TCGA-76-6192      TCGA-76-6193 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6280      TCGA-76-6282      TCGA-76-6283      TCGA-76-6285 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6286      TCGA-76-6656      TCGA-76-6657      TCGA-76-6660 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6661      TCGA-76-6662      TCGA-76-6663      TCGA-76-6664 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-81-5910      TCGA-81-5911      TCGA-87-5896 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PRKCD MUTATED        1      0      0      0
  PRKCD WILD-TYPE     40     38     31     33
D23V7, multiclass
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             142 
     TCGA-02-0003      TCGA-02-2470      TCGA-02-2485      TCGA-06-0126 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0128      TCGA-06-0129      TCGA-06-0130      TCGA-06-0154 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0155      TCGA-06-0189      TCGA-06-0238      TCGA-06-0644 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0650      TCGA-06-0875      TCGA-06-0876      TCGA-06-0877 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0879      TCGA-06-0882      TCGA-06-0939 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-1804      TCGA-06-1806      TCGA-06-2557      TCGA-06-2558 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2559      TCGA-06-2562      TCGA-06-2563      TCGA-06-2564 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2565      TCGA-06-2567      TCGA-06-2570      TCGA-06-5408 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6699      TCGA-06-6700      TCGA-06-6701      TCGA-08-0386 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0692      TCGA-12-1597      TCGA-12-3649      TCGA-12-3650 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-3652      TCGA-12-3653      TCGA-12-5295      TCGA-12-5301 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0813      TCGA-14-0862      TCGA-14-0871      TCGA-14-1823 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-16-0846      TCGA-19-1390      TCGA-19-1790      TCGA-19-2619 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-2620      TCGA-19-2625      TCGA-19-2631      TCGA-19-4068 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5947      TCGA-19-5950      TCGA-19-5951      TCGA-19-5952 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5953      TCGA-19-5954      TCGA-19-5955      TCGA-19-5958 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5959      TCGA-19-5960      TCGA-26-1442      TCGA-26-5132 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5134      TCGA-26-6173      TCGA-26-6174      TCGA-27-1830 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1833      TCGA-27-1834 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1836      TCGA-27-2518      TCGA-27-2528      TCGA-28-1747 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2501      TCGA-28-5208      TCGA-28-5214 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-1970      TCGA-32-1982      TCGA-32-1986      TCGA-32-1991 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-4210      TCGA-32-4211      TCGA-32-5222      TCGA-41-2573 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-2575      TCGA-41-3392      TCGA-41-3393      TCGA-41-3915 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-4097      TCGA-41-5651      TCGA-41-6646      TCGA-74-6573 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-74-6575      TCGA-74-6577      TCGA-74-6578      TCGA-74-6584 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4926      TCGA-76-4927      TCGA-76-4928      TCGA-76-4929 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4931      TCGA-76-4932      TCGA-76-6192      TCGA-76-6193 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6282      TCGA-76-6283      TCGA-76-6285      TCGA-76-6656 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6657      TCGA-76-6660      TCGA-76-6662      TCGA-76-6663 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6664      TCGA-81-5910 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRKCD MUTATED        0      1      0
  PRKCD WILD-TYPE     48     51     43
D23V8, multiclass
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             142 
     TCGA-02-0003      TCGA-02-2470      TCGA-02-2485      TCGA-06-0126 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0128      TCGA-06-0129      TCGA-06-0130      TCGA-06-0154 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0155      TCGA-06-0189      TCGA-06-0238      TCGA-06-0644 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0650      TCGA-06-0875      TCGA-06-0876      TCGA-06-0877 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0879      TCGA-06-0882      TCGA-06-0939 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-1804      TCGA-06-1806      TCGA-06-2557      TCGA-06-2558 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2559      TCGA-06-2562      TCGA-06-2563      TCGA-06-2564 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2565      TCGA-06-2567      TCGA-06-2570      TCGA-06-5408 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5410      TCGA-06-5411      TCGA-06-5412      TCGA-06-5413 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5414      TCGA-06-5415      TCGA-06-5417      TCGA-06-5418 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5856      TCGA-06-5858      TCGA-06-5859      TCGA-06-6388 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6389      TCGA-06-6390      TCGA-06-6391      TCGA-06-6693 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6694      TCGA-06-6695      TCGA-06-6697      TCGA-06-6698 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-6699      TCGA-06-6700      TCGA-06-6701      TCGA-08-0386 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0692      TCGA-12-1597      TCGA-12-3649      TCGA-12-3650 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-3652      TCGA-12-3653      TCGA-12-5295      TCGA-12-5301 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0813      TCGA-14-0862      TCGA-14-0871      TCGA-14-1823 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-16-0846      TCGA-19-1390      TCGA-19-1790      TCGA-19-2619 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-2620      TCGA-19-2625      TCGA-19-2631      TCGA-19-4068 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5947      TCGA-19-5950      TCGA-19-5951      TCGA-19-5952 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5953      TCGA-19-5954      TCGA-19-5955      TCGA-19-5958 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5959      TCGA-19-5960      TCGA-26-1442      TCGA-26-5132 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5134      TCGA-26-6173      TCGA-26-6174      TCGA-27-1830 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1833      TCGA-27-1834 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1836      TCGA-27-2518      TCGA-27-2528      TCGA-28-1747 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2501      TCGA-28-5208      TCGA-28-5214 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-1970      TCGA-32-1982      TCGA-32-1986      TCGA-32-1991 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-4210      TCGA-32-4211      TCGA-32-5222      TCGA-41-2573 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-2575      TCGA-41-3392      TCGA-41-3393      TCGA-41-3915 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-4097      TCGA-41-5651      TCGA-41-6646      TCGA-74-6573 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-74-6575      TCGA-74-6577      TCGA-74-6578      TCGA-74-6584 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4926      TCGA-76-4927      TCGA-76-4928      TCGA-76-4929 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4931      TCGA-76-4932      TCGA-76-6192      TCGA-76-6193 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6282      TCGA-76-6283      TCGA-76-6285      TCGA-76-6656 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6657      TCGA-76-6660      TCGA-76-6662      TCGA-76-6663 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-6664      TCGA-81-5910 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRKCD MUTATED        1      0      0
  PRKCD WILD-TYPE     43     62     35
D23V9, multiclass
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             140 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0619      TCGA-12-0821      TCGA-12-1597 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-3650      TCGA-12-3652      TCGA-12-3653      TCGA-12-5295 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-5299      TCGA-14-0781      TCGA-14-0787      TCGA-14-0789 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0790      TCGA-14-0817      TCGA-14-1823      TCGA-14-1825 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-1829      TCGA-14-2554      TCGA-15-0742      TCGA-15-1444 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-16-0846      TCGA-16-1045      TCGA-19-1390      TCGA-19-2619 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-2620      TCGA-19-2624      TCGA-19-2625      TCGA-19-2629 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5960      TCGA-26-1442      TCGA-26-5132      TCGA-26-5134 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5135      TCGA-26-5136      TCGA-26-5139      TCGA-27-1830 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1834      TCGA-27-1835 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1837      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2528      TCGA-28-1747 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2499      TCGA-28-2509      TCGA-28-2510 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5213      TCGA-28-5215 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5216      TCGA-28-5218      TCGA-28-5220      TCGA-32-1970 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-1980      TCGA-32-1982      TCGA-32-2615      TCGA-32-2632 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-2634      TCGA-32-2638      TCGA-32-4213      TCGA-32-5222 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-2571      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4925      TCGA-76-4926      TCGA-76-4927 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4928      TCGA-76-4929      TCGA-76-4931      TCGA-76-4932 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  PRKCD MUTATED        1      0      0
  PRKCD WILD-TYPE     30     86     24
D23V10, multiclass
[1] "Remove cluster labels:" "PRKCD MUTATED"         
clus
  PRKCD MUTATED PRKCD WILD-TYPE 
              1             140 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0619      TCGA-12-0821      TCGA-12-1597 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-3650      TCGA-12-3652      TCGA-12-3653      TCGA-12-5295 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-12-5299      TCGA-14-0781      TCGA-14-0787      TCGA-14-0789 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-0790      TCGA-14-0817      TCGA-14-1823      TCGA-14-1825 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-14-1829      TCGA-14-2554      TCGA-15-0742      TCGA-15-1444 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-16-0846      TCGA-16-1045      TCGA-19-1390      TCGA-19-2619 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-2620      TCGA-19-2624      TCGA-19-2625      TCGA-19-2629 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-19-5960      TCGA-26-1442      TCGA-26-5132      TCGA-26-5134 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-26-5135      TCGA-26-5136      TCGA-26-5139      TCGA-27-1830 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1834      TCGA-27-1835 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-1837      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2528      TCGA-28-1747 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2499      TCGA-28-2509      TCGA-28-2510 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5213      TCGA-28-5215 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-28-5216      TCGA-28-5218      TCGA-28-5220      TCGA-32-1970 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-1980      TCGA-32-1982      TCGA-32-2615      TCGA-32-2632 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-32-2634      TCGA-32-2638      TCGA-32-4213      TCGA-32-5222 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-2571      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4925      TCGA-76-4926      TCGA-76-4927 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 
     TCGA-76-4928      TCGA-76-4929      TCGA-76-4931      TCGA-76-4932 
"PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" "PRKCD WILD-TYPE" 

Clustering(24) Variable = REN MUTATION ANALYSIS
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  REN MUTATED        0      0      2      1
  REN WILD-TYPE     69     43     72     53
D24V1, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           0            69
  CLUS_2           0            43
  CLUS_3           2            72
  CLUS_4           1            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  REN MUTATED        0      0      1      2
  REN WILD-TYPE     63     50     47     77
D24V2, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           0            63
  CLUS_2           0            50
  CLUS_3           1            47
  CLUS_4           2            77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  REN MUTATED        1      1      3      0
  REN WILD-TYPE     76     92     42     60
D24V3, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           1            76
  CLUS_2           1            92
  CLUS_3           3            42
  CLUS_4           0            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  REN MUTATED        4      0      1
  REN WILD-TYPE    134     61     75
D24V4, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           4           134
  CLUS_2           0            61
  CLUS_3           1            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  REN MUTATED        2      1      2
  REN WILD-TYPE     83    106     79
D24V5, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           2            83
  CLUS_2           1           106
  CLUS_3           2            79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  REN MUTATED        1      0      2
  REN WILD-TYPE     34     44     27
D24V6, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           1            34
  CLUS_2           0            44
  CLUS_3           2            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            CLUS_1 CLUS_2 CLUS_3 CLUS_4
  REN MUTATED        1      1      1      1
  REN WILD-TYPE     40     37     30     32
D24V7, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           1            40
  CLUS_2           1            37
  CLUS_3           1            30
  CLUS_4           1            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
  REN MUTATED        2      1      1
  REN WILD-TYPE     46     51     42
D24V8, multiclass
        clus
vv       REN MUTATED REN WILD-TYPE
  CLUS_1           2            46
  CLUS_2           1            51
  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"
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  REN MUTATED        0      0      1
  REN WILD-TYPE     44     62     34
D24V9, multiclass
[1] "Remove cluster labels:" "REN MUTATED"           
clus
  REN MUTATED REN WILD-TYPE 
            1           140 
   TCGA-02-0047    TCGA-02-0055    TCGA-02-2483    TCGA-02-2485    TCGA-02-2486 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0129    TCGA-06-0130    TCGA-06-0132    TCGA-06-0141    TCGA-06-0157 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0158    TCGA-06-0168    TCGA-06-0174    TCGA-06-0178    TCGA-06-0184 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0219    TCGA-06-0238    TCGA-06-0644    TCGA-06-0645    TCGA-06-0646 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0649    TCGA-06-0686    TCGA-06-0743    TCGA-06-0744    TCGA-06-0745 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0747    TCGA-06-0749    TCGA-06-0750    TCGA-06-0878    TCGA-06-0882 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-1804    TCGA-06-2557    TCGA-06-2558    TCGA-06-2559    TCGA-06-2561 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-2562    TCGA-06-2563    TCGA-06-2564    TCGA-06-2565    TCGA-06-2567 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-2569    TCGA-06-2570    TCGA-06-5408    TCGA-06-5410    TCGA-06-5412 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-5413    TCGA-06-5414    TCGA-06-5415    TCGA-06-5417    TCGA-06-5418 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-5856    TCGA-06-5858    TCGA-06-5859    TCGA-08-0386    TCGA-12-0616 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-12-0618    TCGA-12-0619    TCGA-12-0821    TCGA-12-1597    TCGA-12-3650 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-12-3652    TCGA-12-3653    TCGA-12-5295    TCGA-12-5299    TCGA-14-0781 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-14-0787    TCGA-14-0789    TCGA-14-0790    TCGA-14-0817    TCGA-14-1823 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-14-1825    TCGA-14-1829    TCGA-14-2554    TCGA-15-0742    TCGA-15-1444 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-16-0846    TCGA-16-1045    TCGA-19-1390    TCGA-19-2619    TCGA-19-2620 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-19-2624    TCGA-19-2625    TCGA-19-2629    TCGA-19-5960    TCGA-26-1442 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-26-5132    TCGA-26-5133    TCGA-26-5134    TCGA-26-5135    TCGA-26-5136 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-26-5139    TCGA-27-1830    TCGA-27-1831    TCGA-27-1832    TCGA-27-1834 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-27-1835    TCGA-27-1837    TCGA-27-2519    TCGA-27-2521    TCGA-27-2523 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-27-2524    TCGA-27-2526    TCGA-27-2528    TCGA-28-1747    TCGA-28-1753 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-28-2499    TCGA-28-2509    TCGA-28-2510    TCGA-28-2513    TCGA-28-2514 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-28-5204    TCGA-28-5207    TCGA-28-5208    TCGA-28-5209    TCGA-28-5213 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-28-5215    TCGA-28-5216    TCGA-28-5218    TCGA-28-5220    TCGA-32-1970 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-32-1980    TCGA-32-1982    TCGA-32-2615    TCGA-32-2632    TCGA-32-2634 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-32-2638    TCGA-32-4213    TCGA-32-5222    TCGA-41-2571    TCGA-41-2572 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-41-3915    TCGA-41-4097    TCGA-41-5651    TCGA-76-4925    TCGA-76-4926 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-76-4927    TCGA-76-4928    TCGA-76-4929    TCGA-76-4931    TCGA-76-4932 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
               vv
clus            CLUS_1 CLUS_2 CLUS_3
  REN MUTATED        0      0      1
  REN WILD-TYPE     31     86     23
D24V10, multiclass
[1] "Remove cluster labels:" "REN MUTATED"           
clus
  REN MUTATED REN WILD-TYPE 
            1           140 
   TCGA-02-0047    TCGA-02-0055    TCGA-02-2483    TCGA-02-2485    TCGA-02-2486 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0129    TCGA-06-0130    TCGA-06-0132    TCGA-06-0141    TCGA-06-0157 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0158    TCGA-06-0168    TCGA-06-0174    TCGA-06-0178    TCGA-06-0184 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0219    TCGA-06-0238    TCGA-06-0644    TCGA-06-0645    TCGA-06-0646 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0649    TCGA-06-0686    TCGA-06-0743    TCGA-06-0744    TCGA-06-0745 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-0747    TCGA-06-0749    TCGA-06-0750    TCGA-06-0878    TCGA-06-0882 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-1804    TCGA-06-2557    TCGA-06-2558    TCGA-06-2559    TCGA-06-2561 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-2562    TCGA-06-2563    TCGA-06-2564    TCGA-06-2565    TCGA-06-2567 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-2569    TCGA-06-2570    TCGA-06-5408    TCGA-06-5410    TCGA-06-5412 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-5413    TCGA-06-5414    TCGA-06-5415    TCGA-06-5417    TCGA-06-5418 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-06-5856    TCGA-06-5858    TCGA-06-5859    TCGA-08-0386    TCGA-12-0616 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-12-0618    TCGA-12-0619    TCGA-12-0821    TCGA-12-1597    TCGA-12-3650 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-12-3652    TCGA-12-3653    TCGA-12-5295    TCGA-12-5299    TCGA-14-0781 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-14-0787    TCGA-14-0789    TCGA-14-0790    TCGA-14-0817    TCGA-14-1823 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-14-1825    TCGA-14-1829    TCGA-14-2554    TCGA-15-0742    TCGA-15-1444 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-16-0846    TCGA-16-1045    TCGA-19-1390    TCGA-19-2619    TCGA-19-2620 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-19-2624    TCGA-19-2625    TCGA-19-2629    TCGA-19-5960    TCGA-26-1442 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-26-5132    TCGA-26-5133    TCGA-26-5134    TCGA-26-5135    TCGA-26-5136 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-26-5139    TCGA-27-1830    TCGA-27-1831    TCGA-27-1832    TCGA-27-1834 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-27-1835    TCGA-27-1837    TCGA-27-2519    TCGA-27-2521    TCGA-27-2523 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-27-2524    TCGA-27-2526    TCGA-27-2528    TCGA-28-1747    TCGA-28-1753 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-28-2499    TCGA-28-2509    TCGA-28-2510    TCGA-28-2513    TCGA-28-2514 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-28-5204    TCGA-28-5207    TCGA-28-5208    TCGA-28-5209    TCGA-28-5213 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-28-5215    TCGA-28-5216    TCGA-28-5218    TCGA-28-5220    TCGA-32-1970 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-32-1980    TCGA-32-1982    TCGA-32-2615    TCGA-32-2632    TCGA-32-2634 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-32-2638    TCGA-32-4213    TCGA-32-5222    TCGA-41-2571    TCGA-41-2572 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-41-3915    TCGA-41-4097    TCGA-41-5651    TCGA-76-4925    TCGA-76-4926 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 
   TCGA-76-4927    TCGA-76-4928    TCGA-76-4929    TCGA-76-4931    TCGA-76-4932 
"REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" "REN WILD-TYPE" 

Clustering(25) Variable = LRRC55 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC55 MUTATED        0      1      3      1
  LRRC55 WILD-TYPE     69     42     71     53
D25V1, multiclass
        clus
vv       LRRC55 MUTATED LRRC55 WILD-TYPE
  CLUS_1              0               69
  CLUS_2              1               42
  CLUS_3              3               71
  CLUS_4              1               53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC55 MUTATED        0      1      1      3
  LRRC55 WILD-TYPE     63     49     47     76
D25V2, multiclass
        clus
vv       LRRC55 MUTATED LRRC55 WILD-TYPE
  CLUS_1              0               63
  CLUS_2              1               49
  CLUS_3              1               47
  CLUS_4              3               76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC55 MUTATED        3      3      0      0
  LRRC55 WILD-TYPE     74     90     45     60
D25V3, multiclass
        clus
vv       LRRC55 MUTATED LRRC55 WILD-TYPE
  CLUS_1              3               74
  CLUS_2              3               90
  CLUS_3              0               45
  CLUS_4              0               60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LRRC55 MUTATED        4      1      1
  LRRC55 WILD-TYPE    134     60     75
D25V4, multiclass
        clus
vv       LRRC55 MUTATED LRRC55 WILD-TYPE
  CLUS_1              4              134
  CLUS_2              1               60
  CLUS_3              1               75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LRRC55 MUTATED        3      3      0
  LRRC55 WILD-TYPE     82    104     81
D25V5, multiclass
        clus
vv       LRRC55 MUTATED LRRC55 WILD-TYPE
  CLUS_1              3               82
  CLUS_2              3              104
  CLUS_3              0               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LRRC55 MUTATED        1      1      0
  LRRC55 WILD-TYPE     34     43     29
D25V6, multiclass
[1] "Remove cluster labels:" "LRRC55 MUTATED"        
clus
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               2              106 
      TCGA-06-0650       TCGA-06-1804       TCGA-06-1806       TCGA-06-5408 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5410       TCGA-06-5411       TCGA-06-5412       TCGA-06-5413 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5415       TCGA-06-5417       TCGA-06-5418       TCGA-06-5856 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5858       TCGA-06-5859       TCGA-06-6388       TCGA-06-6389 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6390       TCGA-06-6391       TCGA-06-6693       TCGA-06-6694 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6695       TCGA-06-6697       TCGA-06-6698       TCGA-06-6699 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6700       TCGA-06-6701       TCGA-12-5295       TCGA-12-5299 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-5301       TCGA-14-0740       TCGA-14-0781       TCGA-14-0862 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-1043       TCGA-14-1395       TCGA-15-1444       TCGA-19-5947 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5950       TCGA-19-5951       TCGA-19-5952       TCGA-19-5953 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5954       TCGA-19-5955       TCGA-19-5958       TCGA-19-5959 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5960       TCGA-26-1442       TCGA-26-5132       TCGA-26-5133 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-5134       TCGA-26-5135       TCGA-26-5136       TCGA-26-5139 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-6173       TCGA-26-6174       TCGA-28-2501       TCGA-28-2510 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5204       TCGA-28-5207       TCGA-28-5208       TCGA-28-5209 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5211       TCGA-28-5213       TCGA-28-5214       TCGA-28-5215 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5216       TCGA-28-5218       TCGA-28-5219       TCGA-28-5220 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-6450       TCGA-32-1979       TCGA-32-1980       TCGA-32-5222 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-5651       TCGA-41-6646       TCGA-74-6573       TCGA-74-6575 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-74-6577       TCGA-74-6578       TCGA-74-6584       TCGA-76-4925 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4926       TCGA-76-4927       TCGA-76-4928       TCGA-76-4929 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4931       TCGA-76-4932       TCGA-76-4934       TCGA-76-4935 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6191       TCGA-76-6192       TCGA-76-6193       TCGA-76-6280 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6282       TCGA-76-6283       TCGA-76-6285       TCGA-76-6286 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6656       TCGA-76-6657       TCGA-76-6660       TCGA-76-6661 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6662       TCGA-76-6663       TCGA-76-6664       TCGA-81-5910 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-81-5911       TCGA-87-5896 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LRRC55 MUTATED        0      1      1      0
  LRRC55 WILD-TYPE     41     37     30     33
D25V7, multiclass
[1] "Remove cluster labels:" "LRRC55 MUTATED"        
clus
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               2              141 
      TCGA-02-0003       TCGA-02-2470       TCGA-02-2485       TCGA-06-0126 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0128       TCGA-06-0129       TCGA-06-0130       TCGA-06-0154 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0155       TCGA-06-0189       TCGA-06-0238       TCGA-06-0644 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0650       TCGA-06-0876       TCGA-06-0877       TCGA-06-0878 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0879       TCGA-06-0882       TCGA-06-0939       TCGA-06-1804 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-1806       TCGA-06-2557       TCGA-06-2558       TCGA-06-2559 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5415 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5417       TCGA-06-5418       TCGA-06-5856       TCGA-06-5858 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5859       TCGA-06-6388       TCGA-06-6389       TCGA-06-6390 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6391       TCGA-06-6693       TCGA-06-6694       TCGA-06-6695 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6697       TCGA-06-6698       TCGA-06-6699       TCGA-06-6700 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6701       TCGA-08-0386       TCGA-12-0692       TCGA-12-1597 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-3649       TCGA-12-3650       TCGA-12-3652       TCGA-12-3653 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-5295       TCGA-12-5301       TCGA-14-0813       TCGA-14-0862 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-0871       TCGA-14-1823       TCGA-16-0846       TCGA-19-1390 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-1790       TCGA-19-2619       TCGA-19-2620       TCGA-19-2625 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-2631       TCGA-19-4068       TCGA-19-5947       TCGA-19-5950 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5951       TCGA-19-5952       TCGA-19-5953       TCGA-19-5954 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5955       TCGA-19-5958       TCGA-19-5959       TCGA-19-5960 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-1442       TCGA-26-5132       TCGA-26-5133       TCGA-26-5134 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-6173       TCGA-26-6174       TCGA-27-1830       TCGA-27-1831 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-1832       TCGA-27-1833       TCGA-27-1834       TCGA-27-1836 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-2518       TCGA-27-2528       TCGA-28-1747       TCGA-28-1753 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-2501       TCGA-28-5208       TCGA-28-5214       TCGA-32-1970 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-1982       TCGA-32-1986       TCGA-32-1991       TCGA-32-4210 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-4211       TCGA-32-5222       TCGA-41-2573       TCGA-41-2575 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-3392       TCGA-41-3393       TCGA-41-3915       TCGA-41-4097 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-5651       TCGA-41-6646       TCGA-74-6573       TCGA-74-6575 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-74-6577       TCGA-74-6578       TCGA-74-6584       TCGA-76-4926 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4927       TCGA-76-4928       TCGA-76-4929       TCGA-76-4931 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4932       TCGA-76-6192       TCGA-76-6193       TCGA-76-6282 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6283       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6660       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-81-5910 
"LRRC55 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LRRC55 MUTATED        0      1      1
  LRRC55 WILD-TYPE     48     51     42
D25V8, multiclass
[1] "Remove cluster labels:" "LRRC55 MUTATED"        
clus
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               2              141 
      TCGA-02-0003       TCGA-02-2470       TCGA-02-2485       TCGA-06-0126 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0128       TCGA-06-0129       TCGA-06-0130       TCGA-06-0154 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0155       TCGA-06-0189       TCGA-06-0238       TCGA-06-0644 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0650       TCGA-06-0876       TCGA-06-0877       TCGA-06-0878 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0879       TCGA-06-0882       TCGA-06-0939       TCGA-06-1804 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-1806       TCGA-06-2557       TCGA-06-2558       TCGA-06-2559 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2562       TCGA-06-2563       TCGA-06-2564       TCGA-06-2565 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2567       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5415 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5417       TCGA-06-5418       TCGA-06-5856       TCGA-06-5858 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5859       TCGA-06-6388       TCGA-06-6389       TCGA-06-6390 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6391       TCGA-06-6693       TCGA-06-6694       TCGA-06-6695 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6697       TCGA-06-6698       TCGA-06-6699       TCGA-06-6700 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-6701       TCGA-08-0386       TCGA-12-0692       TCGA-12-1597 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-3649       TCGA-12-3650       TCGA-12-3652       TCGA-12-3653 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-5295       TCGA-12-5301       TCGA-14-0813       TCGA-14-0862 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-0871       TCGA-14-1823       TCGA-16-0846       TCGA-19-1390 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-1790       TCGA-19-2619       TCGA-19-2620       TCGA-19-2625 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-2631       TCGA-19-4068       TCGA-19-5947       TCGA-19-5950 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5951       TCGA-19-5952       TCGA-19-5953       TCGA-19-5954 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-5955       TCGA-19-5958       TCGA-19-5959       TCGA-19-5960 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-1442       TCGA-26-5132       TCGA-26-5133       TCGA-26-5134 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-6173       TCGA-26-6174       TCGA-27-1830       TCGA-27-1831 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-1832       TCGA-27-1833       TCGA-27-1834       TCGA-27-1836 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-2518       TCGA-27-2528       TCGA-28-1747       TCGA-28-1753 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-2501       TCGA-28-5208       TCGA-28-5214       TCGA-32-1970 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-1982       TCGA-32-1986       TCGA-32-1991       TCGA-32-4210 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-4211       TCGA-32-5222       TCGA-41-2573       TCGA-41-2575 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-3392       TCGA-41-3393       TCGA-41-3915       TCGA-41-4097 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-5651       TCGA-41-6646       TCGA-74-6573       TCGA-74-6575 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-74-6577       TCGA-74-6578       TCGA-74-6584       TCGA-76-4926 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4927       TCGA-76-4928       TCGA-76-4929       TCGA-76-4931 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4932       TCGA-76-6192       TCGA-76-6193       TCGA-76-6282 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6283       TCGA-76-6285       TCGA-76-6656       TCGA-76-6657 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-6660       TCGA-76-6662       TCGA-76-6663       TCGA-76-6664 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-81-5910 
"LRRC55 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LRRC55 MUTATED        0      1      0
  LRRC55 WILD-TYPE     44     61     35
D25V9, multiclass
[1] "Remove cluster labels:" "LRRC55 MUTATED"        
clus
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               1              140 
      TCGA-02-0047       TCGA-02-0055       TCGA-02-2483       TCGA-02-2485 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-02-2486       TCGA-06-0129       TCGA-06-0130       TCGA-06-0132 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0141       TCGA-06-0157       TCGA-06-0158       TCGA-06-0168 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0174       TCGA-06-0178       TCGA-06-0184       TCGA-06-0219 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0238       TCGA-06-0644       TCGA-06-0645       TCGA-06-0646 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0649       TCGA-06-0686       TCGA-06-0743       TCGA-06-0744 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0745       TCGA-06-0747       TCGA-06-0749       TCGA-06-0750 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0882       TCGA-06-1804       TCGA-06-2557 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2558       TCGA-06-2559       TCGA-06-2561       TCGA-06-2562 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2563       TCGA-06-2564       TCGA-06-2565       TCGA-06-2567 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2569       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5415 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5417       TCGA-06-5418       TCGA-06-5856       TCGA-06-5858 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5859       TCGA-08-0386       TCGA-12-0616       TCGA-12-0618 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-0619       TCGA-12-0821       TCGA-12-1597       TCGA-12-3650 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5295       TCGA-12-5299 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-0781       TCGA-14-0787       TCGA-14-0789       TCGA-14-0790 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-0817       TCGA-14-1823       TCGA-14-1825       TCGA-14-1829 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-2554       TCGA-15-0742       TCGA-15-1444       TCGA-16-0846 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-16-1045       TCGA-19-1390       TCGA-19-2619       TCGA-19-2620 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-2624       TCGA-19-2625       TCGA-19-2629       TCGA-19-5960 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-1442       TCGA-26-5132       TCGA-26-5133       TCGA-26-5134 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-5135       TCGA-26-5136       TCGA-26-5139       TCGA-27-1830 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-1831       TCGA-27-1832       TCGA-27-1834       TCGA-27-1835 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-1837       TCGA-27-2519       TCGA-27-2521       TCGA-27-2523 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-2524       TCGA-27-2526       TCGA-27-2528       TCGA-28-1747 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-1753       TCGA-28-2499       TCGA-28-2509       TCGA-28-2510 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-2513       TCGA-28-2514       TCGA-28-5204       TCGA-28-5207 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5208       TCGA-28-5209       TCGA-28-5213       TCGA-28-5215 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5216       TCGA-28-5218       TCGA-28-5220       TCGA-32-1970 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-1980       TCGA-32-1982       TCGA-32-2615       TCGA-32-2632 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-2634       TCGA-32-2638       TCGA-32-4213       TCGA-32-5222 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-2571       TCGA-41-2572       TCGA-41-3915       TCGA-41-4097 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-5651       TCGA-76-4925       TCGA-76-4926       TCGA-76-4927 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4928       TCGA-76-4929       TCGA-76-4931       TCGA-76-4932 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  LRRC55 MUTATED        0      1      0
  LRRC55 WILD-TYPE     31     85     24
D25V10, multiclass
[1] "Remove cluster labels:" "LRRC55 MUTATED"        
clus
  LRRC55 MUTATED LRRC55 WILD-TYPE 
               1              140 
      TCGA-02-0047       TCGA-02-0055       TCGA-02-2483       TCGA-02-2485 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-02-2486       TCGA-06-0129       TCGA-06-0130       TCGA-06-0132 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0141       TCGA-06-0157       TCGA-06-0158       TCGA-06-0168 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0174       TCGA-06-0178       TCGA-06-0184       TCGA-06-0219 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0238       TCGA-06-0644       TCGA-06-0645       TCGA-06-0646 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0649       TCGA-06-0686       TCGA-06-0743       TCGA-06-0744 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0745       TCGA-06-0747       TCGA-06-0749       TCGA-06-0750 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-0878       TCGA-06-0882       TCGA-06-1804       TCGA-06-2557 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2558       TCGA-06-2559       TCGA-06-2561       TCGA-06-2562 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2563       TCGA-06-2564       TCGA-06-2565       TCGA-06-2567 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-2569       TCGA-06-2570       TCGA-06-5408       TCGA-06-5410 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5411       TCGA-06-5412       TCGA-06-5413       TCGA-06-5415 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5417       TCGA-06-5418       TCGA-06-5856       TCGA-06-5858 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-06-5859       TCGA-08-0386       TCGA-12-0616       TCGA-12-0618 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-0619       TCGA-12-0821       TCGA-12-1597       TCGA-12-3650 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-12-3652       TCGA-12-3653       TCGA-12-5295       TCGA-12-5299 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-0781       TCGA-14-0787       TCGA-14-0789       TCGA-14-0790 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-0817       TCGA-14-1823       TCGA-14-1825       TCGA-14-1829 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-14-2554       TCGA-15-0742       TCGA-15-1444       TCGA-16-0846 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-16-1045       TCGA-19-1390       TCGA-19-2619       TCGA-19-2620 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-19-2624       TCGA-19-2625       TCGA-19-2629       TCGA-19-5960 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-1442       TCGA-26-5132       TCGA-26-5133       TCGA-26-5134 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-26-5135       TCGA-26-5136       TCGA-26-5139       TCGA-27-1830 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-1831       TCGA-27-1832       TCGA-27-1834       TCGA-27-1835 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-1837       TCGA-27-2519       TCGA-27-2521       TCGA-27-2523 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-27-2524       TCGA-27-2526       TCGA-27-2528       TCGA-28-1747 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-1753       TCGA-28-2499       TCGA-28-2509       TCGA-28-2510 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-2513       TCGA-28-2514       TCGA-28-5204       TCGA-28-5207 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5208       TCGA-28-5209       TCGA-28-5213       TCGA-28-5215 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-28-5216       TCGA-28-5218       TCGA-28-5220       TCGA-32-1970 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-1980       TCGA-32-1982       TCGA-32-2615       TCGA-32-2632 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-32-2634       TCGA-32-2638       TCGA-32-4213       TCGA-32-5222 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-2571       TCGA-41-2572       TCGA-41-3915       TCGA-41-4097 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-41-5651       TCGA-76-4925       TCGA-76-4926       TCGA-76-4927 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 
      TCGA-76-4928       TCGA-76-4929       TCGA-76-4931       TCGA-76-4932 
"LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" "LRRC55 WILD-TYPE" 

Clustering(26) Variable = MUC17 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC17 MUTATED       10      5      1      3
  MUC17 WILD-TYPE     59     38     73     51
D26V1, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1            10              59
  CLUS_2             5              38
  CLUS_3             1              73
  CLUS_4             3              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC17 MUTATED        8      1      3      7
  MUC17 WILD-TYPE     55     49     45     72
D26V2, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             8              55
  CLUS_2             1              49
  CLUS_3             3              45
  CLUS_4             7              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC17 MUTATED        5      7      3      7
  MUC17 WILD-TYPE     72     86     42     53
D26V3, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             5              72
  CLUS_2             7              86
  CLUS_3             3              42
  CLUS_4             7              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC17 MUTATED       10      4      8
  MUC17 WILD-TYPE    128     57     68
D26V4, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1            10             128
  CLUS_2             4              57
  CLUS_3             8              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
  MUC17 MUTATED        7      8      7
  MUC17 WILD-TYPE     78     99     74
D26V5, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             7              78
  CLUS_2             8              99
  CLUS_3             7              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC17 MUTATED        4      5      1
  MUC17 WILD-TYPE     31     39     28
D26V6, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             4              31
  CLUS_2             5              39
  CLUS_3             1              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  MUC17 MUTATED        5      1      1      4
  MUC17 WILD-TYPE     36     37     30     29
D26V7, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             5              36
  CLUS_2             1              37
  CLUS_3             1              30
  CLUS_4             4              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
  MUC17 MUTATED        6      3      2
  MUC17 WILD-TYPE     42     49     41
D26V8, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             6              42
  CLUS_2             3              49
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC17 MUTATED        4      6      2
  MUC17 WILD-TYPE     40     56     33
D26V9, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             4              40
  CLUS_2             6              56
  CLUS_3             2              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  MUC17 MUTATED        2      8      2
  MUC17 WILD-TYPE     29     78     22
D26V10, multiclass
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  CLUS_1             2              29
  CLUS_2             8              78
  CLUS_3             2              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = CD209 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD209 MUTATED        1      0      2      1
  CD209 WILD-TYPE     68     43     72     53
D27V1, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             1              68
  CLUS_2             0              43
  CLUS_3             2              72
  CLUS_4             1              53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD209 MUTATED        1      1      1      1
  CD209 WILD-TYPE     62     49     47     78
D27V2, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             1              62
  CLUS_2             1              49
  CLUS_3             1              47
  CLUS_4             1              78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD209 MUTATED        2      0      0      3
  CD209 WILD-TYPE     75     93     45     57
D27V3, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             2              75
  CLUS_2             0              93
  CLUS_3             0              45
  CLUS_4             3              57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD209 MUTATED        3      0      2
  CD209 WILD-TYPE    135     61     74
D27V4, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             3             135
  CLUS_2             0              61
  CLUS_3             2              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD209 MUTATED        1      1      2
  CD209 WILD-TYPE     84    106     79
D27V5, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             1              84
  CLUS_2             1             106
  CLUS_3             2              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD209 MUTATED        2      1      0
  CD209 WILD-TYPE     33     43     29
D27V6, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             2              33
  CLUS_2             1              43
  CLUS_3             0              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD209 MUTATED        1      0      1      2
  CD209 WILD-TYPE     40     38     30     31
D27V7, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             0              38
  CLUS_3             1              30
  CLUS_4             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD209 MUTATED        1      2      1
  CD209 WILD-TYPE     47     50     42
D27V8, multiclass
        clus
vv       CD209 MUTATED CD209 WILD-TYPE
  CLUS_1             1              47
  CLUS_2             2              50
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD209 MUTATED        1      0      1
  CD209 WILD-TYPE     43     62     34
D27V9, multiclass
[1] "Remove cluster labels:" "CD209 MUTATED"         
clus
  CD209 MUTATED CD209 WILD-TYPE 
              2             139 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0619      TCGA-12-0821      TCGA-12-1597 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-12-3650      TCGA-12-3652      TCGA-12-3653      TCGA-12-5295 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-12-5299      TCGA-14-0781      TCGA-14-0787      TCGA-14-0789 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-14-0790      TCGA-14-0817      TCGA-14-1823      TCGA-14-1825 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-14-1829      TCGA-14-2554      TCGA-15-0742      TCGA-15-1444 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-16-0846      TCGA-16-1045      TCGA-19-1390      TCGA-19-2619 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-19-2620      TCGA-19-2624      TCGA-19-2625      TCGA-19-2629 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-19-5960      TCGA-26-1442      TCGA-26-5132      TCGA-26-5133 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-26-5134      TCGA-26-5135      TCGA-26-5136      TCGA-26-5139 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-27-1830      TCGA-27-1831      TCGA-27-1832      TCGA-27-1834 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-27-1835      TCGA-27-1837      TCGA-27-2519      TCGA-27-2521 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-27-2523      TCGA-27-2524      TCGA-27-2526      TCGA-27-2528 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-1747      TCGA-28-1753      TCGA-28-2499      TCGA-28-2509 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-2510      TCGA-28-2513      TCGA-28-2514      TCGA-28-5204 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-5207      TCGA-28-5208      TCGA-28-5209      TCGA-28-5213 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-5215      TCGA-28-5216      TCGA-28-5218      TCGA-28-5220 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-32-1970      TCGA-32-1980      TCGA-32-1982      TCGA-32-2615 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-32-2632      TCGA-32-2634      TCGA-32-2638      TCGA-32-4213 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-32-5222      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4925      TCGA-76-4926      TCGA-76-4927 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-76-4928      TCGA-76-4929      TCGA-76-4932 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  CD209 MUTATED        1      0      1
  CD209 WILD-TYPE     30     86     23
D27V10, multiclass
[1] "Remove cluster labels:" "CD209 MUTATED"         
clus
  CD209 MUTATED CD209 WILD-TYPE 
              2             139 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0619      TCGA-12-0821      TCGA-12-1597 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-12-3650      TCGA-12-3652      TCGA-12-3653      TCGA-12-5295 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-12-5299      TCGA-14-0781      TCGA-14-0787      TCGA-14-0789 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-14-0790      TCGA-14-0817      TCGA-14-1823      TCGA-14-1825 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-14-1829      TCGA-14-2554      TCGA-15-0742      TCGA-15-1444 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-16-0846      TCGA-16-1045      TCGA-19-1390      TCGA-19-2619 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-19-2620      TCGA-19-2624      TCGA-19-2625      TCGA-19-2629 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-19-5960      TCGA-26-1442      TCGA-26-5132      TCGA-26-5133 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-26-5134      TCGA-26-5135      TCGA-26-5136      TCGA-26-5139 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-27-1830      TCGA-27-1831      TCGA-27-1832      TCGA-27-1834 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-27-1835      TCGA-27-1837      TCGA-27-2519      TCGA-27-2521 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-27-2523      TCGA-27-2524      TCGA-27-2526      TCGA-27-2528 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-1747      TCGA-28-1753      TCGA-28-2499      TCGA-28-2509 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-2510      TCGA-28-2513      TCGA-28-2514      TCGA-28-5204 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-5207      TCGA-28-5208      TCGA-28-5209      TCGA-28-5213 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-28-5215      TCGA-28-5216      TCGA-28-5218      TCGA-28-5220 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-32-1970      TCGA-32-1980      TCGA-32-1982      TCGA-32-2615 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-32-2632      TCGA-32-2634      TCGA-32-2638      TCGA-32-4213 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-32-5222      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4925      TCGA-76-4926      TCGA-76-4927 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 
     TCGA-76-4928      TCGA-76-4929      TCGA-76-4932 
"CD209 WILD-TYPE" "CD209 WILD-TYPE" "CD209 WILD-TYPE" 

Clustering(28) Variable = DDX5 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DDX5 MUTATED        1      0      0      2
  DDX5 WILD-TYPE     68     43     74     52
D28V1, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            0             43
  CLUS_3            0             74
  CLUS_4            2             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DDX5 MUTATED        1      1      0      1
  DDX5 WILD-TYPE     62     49     48     78
D28V2, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            1             62
  CLUS_2            1             49
  CLUS_3            0             48
  CLUS_4            1             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DDX5 MUTATED        0      2      1      1
  DDX5 WILD-TYPE     77     91     44     59
D28V3, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            0             77
  CLUS_2            2             91
  CLUS_3            1             44
  CLUS_4            1             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        1      1      2
  DDX5 WILD-TYPE    137     60     74
D28V4, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            1            137
  CLUS_2            1             60
  CLUS_3            2             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        0      1      3
  DDX5 WILD-TYPE     85    106     78
D28V5, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            0             85
  CLUS_2            1            106
  CLUS_3            3             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
  DDX5 MUTATED        0      2      0
  DDX5 WILD-TYPE     35     42     29
D28V6, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             2            106 
    TCGA-06-0650     TCGA-06-1804     TCGA-06-1806     TCGA-06-5408 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5410     TCGA-06-5411     TCGA-06-5412     TCGA-06-5413 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5414     TCGA-06-5415     TCGA-06-5417     TCGA-06-5418 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5856     TCGA-06-5858     TCGA-06-5859     TCGA-06-6388 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6389     TCGA-06-6390     TCGA-06-6391     TCGA-06-6693 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6694     TCGA-06-6695     TCGA-06-6697     TCGA-06-6698 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6699     TCGA-06-6700     TCGA-06-6701     TCGA-12-5295 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-5299     TCGA-12-5301     TCGA-14-0740     TCGA-14-0781 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0862     TCGA-14-1043     TCGA-14-1395     TCGA-14-1450 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-15-1444     TCGA-19-5947     TCGA-19-5950     TCGA-19-5951 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5952     TCGA-19-5953     TCGA-19-5954     TCGA-19-5955 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5958     TCGA-19-5959     TCGA-19-5960     TCGA-26-1442 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5132     TCGA-26-5133     TCGA-26-5134     TCGA-26-5135 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5136     TCGA-26-5139     TCGA-26-6173     TCGA-26-6174 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-2501     TCGA-28-2510     TCGA-28-5204     TCGA-28-5207 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5208     TCGA-28-5209     TCGA-28-5211     TCGA-28-5213 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5214     TCGA-28-5215     TCGA-28-5216     TCGA-28-5218 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5219     TCGA-28-5220     TCGA-28-6450     TCGA-32-1979 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-1980     TCGA-32-5222     TCGA-41-5651     TCGA-41-6646 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-74-6573     TCGA-74-6575     TCGA-74-6577     TCGA-74-6578 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-74-6584     TCGA-76-4926     TCGA-76-4927     TCGA-76-4928 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4929     TCGA-76-4931     TCGA-76-4932     TCGA-76-4934 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4935     TCGA-76-6191     TCGA-76-6192     TCGA-76-6193 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6280     TCGA-76-6282     TCGA-76-6283     TCGA-76-6285 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6286     TCGA-76-6656     TCGA-76-6657     TCGA-76-6661 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6662     TCGA-76-6663     TCGA-76-6664     TCGA-81-5910 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-81-5911     TCGA-87-5896 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  DDX5 MUTATED        2      0      0      0
  DDX5 WILD-TYPE     39     38     31     33
D28V7, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             2            141 
    TCGA-02-0003     TCGA-02-2470     TCGA-02-2485     TCGA-06-0126 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0128     TCGA-06-0129     TCGA-06-0130     TCGA-06-0154 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0155     TCGA-06-0189     TCGA-06-0238     TCGA-06-0644 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0650     TCGA-06-0875     TCGA-06-0876     TCGA-06-0877 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0879     TCGA-06-0882     TCGA-06-0939 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-1804     TCGA-06-1806     TCGA-06-2557     TCGA-06-2558 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2559     TCGA-06-2562     TCGA-06-2563     TCGA-06-2564 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2565     TCGA-06-2567     TCGA-06-2570     TCGA-06-5408 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5410     TCGA-06-5411     TCGA-06-5412     TCGA-06-5413 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5414     TCGA-06-5415     TCGA-06-5417     TCGA-06-5418 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5856     TCGA-06-5858     TCGA-06-5859     TCGA-06-6388 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6389     TCGA-06-6390     TCGA-06-6391     TCGA-06-6693 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6694     TCGA-06-6695     TCGA-06-6697     TCGA-06-6698 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6699     TCGA-06-6700     TCGA-06-6701     TCGA-08-0386 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-0692     TCGA-12-1597     TCGA-12-3649     TCGA-12-3650 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5295     TCGA-12-5301 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0813     TCGA-14-0862     TCGA-14-0871     TCGA-14-1823 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-16-0846     TCGA-19-1390     TCGA-19-1790     TCGA-19-2619 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-2620     TCGA-19-2625     TCGA-19-2631     TCGA-19-4068 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5947     TCGA-19-5950     TCGA-19-5951     TCGA-19-5952 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5953     TCGA-19-5954     TCGA-19-5955     TCGA-19-5958 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5959     TCGA-19-5960     TCGA-26-1442     TCGA-26-5132 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5133     TCGA-26-5134     TCGA-26-6173     TCGA-26-6174 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1830     TCGA-27-1831     TCGA-27-1832     TCGA-27-1833 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1834     TCGA-27-1836     TCGA-27-2518     TCGA-27-2528 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-1747     TCGA-28-1753     TCGA-28-2501     TCGA-28-5208 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5214     TCGA-32-1970     TCGA-32-1982     TCGA-32-1991 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-4210     TCGA-32-4211     TCGA-32-5222     TCGA-41-2573 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-2575     TCGA-41-3392     TCGA-41-3393     TCGA-41-3915 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-4097     TCGA-41-5651     TCGA-41-6646     TCGA-74-6573 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-74-6575     TCGA-74-6577     TCGA-74-6578     TCGA-74-6584 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4926     TCGA-76-4927     TCGA-76-4928     TCGA-76-4929 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-6192     TCGA-76-6193 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6283     TCGA-76-6285     TCGA-76-6656 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6657     TCGA-76-6662     TCGA-76-6663     TCGA-76-6664 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-81-5910 
"DDX5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        2      0      0
  DDX5 WILD-TYPE     46     52     43
D28V8, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             2            141 
    TCGA-02-0003     TCGA-02-2470     TCGA-02-2485     TCGA-06-0126 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0128     TCGA-06-0129     TCGA-06-0130     TCGA-06-0154 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0155     TCGA-06-0189     TCGA-06-0238     TCGA-06-0644 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0650     TCGA-06-0875     TCGA-06-0876     TCGA-06-0877 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0879     TCGA-06-0882     TCGA-06-0939 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-1804     TCGA-06-1806     TCGA-06-2557     TCGA-06-2558 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2559     TCGA-06-2562     TCGA-06-2563     TCGA-06-2564 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2565     TCGA-06-2567     TCGA-06-2570     TCGA-06-5408 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5410     TCGA-06-5411     TCGA-06-5412     TCGA-06-5413 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5414     TCGA-06-5415     TCGA-06-5417     TCGA-06-5418 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5856     TCGA-06-5858     TCGA-06-5859     TCGA-06-6388 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6389     TCGA-06-6390     TCGA-06-6391     TCGA-06-6693 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6694     TCGA-06-6695     TCGA-06-6697     TCGA-06-6698 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-6699     TCGA-06-6700     TCGA-06-6701     TCGA-08-0386 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-0692     TCGA-12-1597     TCGA-12-3649     TCGA-12-3650 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5295     TCGA-12-5301 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0813     TCGA-14-0862     TCGA-14-0871     TCGA-14-1823 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-16-0846     TCGA-19-1390     TCGA-19-1790     TCGA-19-2619 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-2620     TCGA-19-2625     TCGA-19-2631     TCGA-19-4068 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5947     TCGA-19-5950     TCGA-19-5951     TCGA-19-5952 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5953     TCGA-19-5954     TCGA-19-5955     TCGA-19-5958 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5959     TCGA-19-5960     TCGA-26-1442     TCGA-26-5132 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5133     TCGA-26-5134     TCGA-26-6173     TCGA-26-6174 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1830     TCGA-27-1831     TCGA-27-1832     TCGA-27-1833 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1834     TCGA-27-1836     TCGA-27-2518     TCGA-27-2528 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-1747     TCGA-28-1753     TCGA-28-2501     TCGA-28-5208 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5214     TCGA-32-1970     TCGA-32-1982     TCGA-32-1991 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-4210     TCGA-32-4211     TCGA-32-5222     TCGA-41-2573 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-2575     TCGA-41-3392     TCGA-41-3393     TCGA-41-3915 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-4097     TCGA-41-5651     TCGA-41-6646     TCGA-74-6573 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-74-6575     TCGA-74-6577     TCGA-74-6578     TCGA-74-6584 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4926     TCGA-76-4927     TCGA-76-4928     TCGA-76-4929 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-6192     TCGA-76-6193 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6283     TCGA-76-6285     TCGA-76-6656 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-6657     TCGA-76-6662     TCGA-76-6663     TCGA-76-6664 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-81-5910 
"DDX5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        0      1      0
  DDX5 WILD-TYPE     44     61     35
D28V9, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             1            140 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0219 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0644     TCGA-06-0645     TCGA-06-0646 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0649     TCGA-06-0686     TCGA-06-0743     TCGA-06-0744 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0749     TCGA-06-0750 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0882     TCGA-06-1804     TCGA-06-2557 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5408     TCGA-06-5410 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-08-0386     TCGA-12-0616 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-0618     TCGA-12-0619     TCGA-12-0821     TCGA-12-1597 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-3650     TCGA-12-3652     TCGA-12-3653     TCGA-12-5295 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-5299     TCGA-14-0781     TCGA-14-0787     TCGA-14-0789 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0790     TCGA-14-0817     TCGA-14-1823     TCGA-14-1825 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-1829     TCGA-14-2554     TCGA-15-0742     TCGA-15-1444 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-16-0846     TCGA-16-1045     TCGA-19-1390     TCGA-19-2619 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-2620     TCGA-19-2624     TCGA-19-2625     TCGA-19-2629 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5960     TCGA-26-1442     TCGA-26-5132     TCGA-26-5133 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5134     TCGA-26-5135     TCGA-26-5136     TCGA-26-5139 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1830     TCGA-27-1831     TCGA-27-1832     TCGA-27-1834 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1835     TCGA-27-1837     TCGA-27-2519     TCGA-27-2521 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-2523     TCGA-27-2524     TCGA-27-2526     TCGA-27-2528 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-1747     TCGA-28-1753     TCGA-28-2499     TCGA-28-2509 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-2510     TCGA-28-2513     TCGA-28-2514     TCGA-28-5204 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5207     TCGA-28-5208     TCGA-28-5209     TCGA-28-5213 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5215     TCGA-28-5216     TCGA-28-5218     TCGA-28-5220 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-1970     TCGA-32-1980     TCGA-32-1982     TCGA-32-2615 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-2632     TCGA-32-2634     TCGA-32-2638     TCGA-32-4213 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-5222     TCGA-41-2571     TCGA-41-2572     TCGA-41-3915 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-4097     TCGA-41-5651     TCGA-76-4926     TCGA-76-4927 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4928     TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  DDX5 MUTATED        0      1      0
  DDX5 WILD-TYPE     31     85     24
D28V10, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             1            140 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0219 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0644     TCGA-06-0645     TCGA-06-0646 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0649     TCGA-06-0686     TCGA-06-0743     TCGA-06-0744 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0749     TCGA-06-0750 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0882     TCGA-06-1804     TCGA-06-2557 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5408     TCGA-06-5410 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-08-0386     TCGA-12-0616 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-0618     TCGA-12-0619     TCGA-12-0821     TCGA-12-1597 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-3650     TCGA-12-3652     TCGA-12-3653     TCGA-12-5295 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-12-5299     TCGA-14-0781     TCGA-14-0787     TCGA-14-0789 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-0790     TCGA-14-0817     TCGA-14-1823     TCGA-14-1825 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-14-1829     TCGA-14-2554     TCGA-15-0742     TCGA-15-1444 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-16-0846     TCGA-16-1045     TCGA-19-1390     TCGA-19-2619 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-2620     TCGA-19-2624     TCGA-19-2625     TCGA-19-2629 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-19-5960     TCGA-26-1442     TCGA-26-5132     TCGA-26-5133 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-26-5134     TCGA-26-5135     TCGA-26-5136     TCGA-26-5139 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1830     TCGA-27-1831     TCGA-27-1832     TCGA-27-1834 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-1835     TCGA-27-1837     TCGA-27-2519     TCGA-27-2521 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-27-2523     TCGA-27-2524     TCGA-27-2526     TCGA-27-2528 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-1747     TCGA-28-1753     TCGA-28-2499     TCGA-28-2509 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-2510     TCGA-28-2513     TCGA-28-2514     TCGA-28-5204 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5207     TCGA-28-5208     TCGA-28-5209     TCGA-28-5213 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-28-5215     TCGA-28-5216     TCGA-28-5218     TCGA-28-5220 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-1970     TCGA-32-1980     TCGA-32-1982     TCGA-32-2615 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-2632     TCGA-32-2634     TCGA-32-2638     TCGA-32-4213 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-32-5222     TCGA-41-2571     TCGA-41-2572     TCGA-41-3915 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-41-4097     TCGA-41-5651     TCGA-76-4926     TCGA-76-4927 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-76-4928     TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 

Clustering(29) Variable = TP63 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP63 MUTATED        1      1      2      1
  TP63 WILD-TYPE     68     42     72     53
D29V1, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            1             42
  CLUS_3            2             72
  CLUS_4            1             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP63 MUTATED        1      1      2      1
  TP63 WILD-TYPE     62     49     46     78
D29V2, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            1             62
  CLUS_2            1             49
  CLUS_3            2             46
  CLUS_4            1             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP63 MUTATED        1      1      1      3
  TP63 WILD-TYPE     76     92     44     57
D29V3, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            1             76
  CLUS_2            1             92
  CLUS_3            1             44
  CLUS_4            3             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP63 MUTATED        2      2      2
  TP63 WILD-TYPE    136     59     74
D29V4, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            2            136
  CLUS_2            2             59
  CLUS_3            2             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP63 MUTATED        1      3      2
  TP63 WILD-TYPE     84    104     79
D29V5, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            1             84
  CLUS_2            3            104
  CLUS_3            2             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP63 MUTATED        2      2      0
  TP63 WILD-TYPE     33     42     29
D29V6, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            2             33
  CLUS_2            2             42
  CLUS_3            0             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP63 MUTATED        0      1      0      3
  TP63 WILD-TYPE     41     37     31     30
D29V7, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            1             37
  CLUS_3            0             31
  CLUS_4            3             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
  TP63 MUTATED        3      1      0
  TP63 WILD-TYPE     45     51     43
D29V8, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            3             45
  CLUS_2            1             51
  CLUS_3            0             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP63 MUTATED        0      1      2
  TP63 WILD-TYPE     44     61     33
D29V9, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            0             44
  CLUS_2            1             61
  CLUS_3            2             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP63 MUTATED        0      1      2
  TP63 WILD-TYPE     31     85     22
D29V10, multiclass
        clus
vv       TP63 MUTATED TP63 WILD-TYPE
  CLUS_1            0             31
  CLUS_2            1             85
  CLUS_3            2             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = CD1D MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD1D MUTATED        1      1      1      0
  CD1D WILD-TYPE     68     42     73     54
D30V1, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            1             68
  CLUS_2            1             42
  CLUS_3            1             73
  CLUS_4            0             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD1D MUTATED        1      1      0      1
  CD1D WILD-TYPE     62     49     48     78
D30V2, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            1             62
  CLUS_2            1             49
  CLUS_3            0             48
  CLUS_4            1             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD1D MUTATED        2      2      0      0
  CD1D WILD-TYPE     75     91     45     60
D30V3, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            2             75
  CLUS_2            2             91
  CLUS_3            0             45
  CLUS_4            0             60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CD1D MUTATED        1      0      3
  CD1D WILD-TYPE    137     61     73
D30V4, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            1            137
  CLUS_2            0             61
  CLUS_3            3             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
  CD1D MUTATED        2      1      1
  CD1D WILD-TYPE     83    106     80
D30V5, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            2             83
  CLUS_2            1            106
  CLUS_3            1             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CD1D MUTATED        1      1      1
  CD1D WILD-TYPE     34     43     28
D30V6, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            1             34
  CLUS_2            1             43
  CLUS_3            1             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CD1D MUTATED        1      1      1      0
  CD1D WILD-TYPE     40     37     30     33
D30V7, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            1             40
  CLUS_2            1             37
  CLUS_3            1             30
  CLUS_4            0             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
  CD1D MUTATED        1      1      1
  CD1D WILD-TYPE     47     51     42
D30V8, multiclass
        clus
vv       CD1D MUTATED CD1D WILD-TYPE
  CLUS_1            1             47
  CLUS_2            1             51
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CD1D MUTATED        0      1      0
  CD1D WILD-TYPE     44     61     35
D30V9, multiclass
[1] "Remove cluster labels:" "CD1D MUTATED"          
clus
  CD1D MUTATED CD1D WILD-TYPE 
             1            140 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0219     TCGA-06-0238 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0644     TCGA-06-0645     TCGA-06-0646     TCGA-06-0649 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0686     TCGA-06-0743     TCGA-06-0744     TCGA-06-0745 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0747     TCGA-06-0749     TCGA-06-0750     TCGA-06-0878 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0882     TCGA-06-1804     TCGA-06-2557     TCGA-06-2558 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-2559     TCGA-06-2561     TCGA-06-2562     TCGA-06-2563 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-2564     TCGA-06-2565     TCGA-06-2567     TCGA-06-2569 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-2570     TCGA-06-5408     TCGA-06-5410     TCGA-06-5411 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-5412     TCGA-06-5413     TCGA-06-5414     TCGA-06-5415 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-5417     TCGA-06-5418     TCGA-06-5856     TCGA-06-5858 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-5859     TCGA-08-0386     TCGA-12-0616     TCGA-12-0618 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-12-0619     TCGA-12-0821     TCGA-12-1597     TCGA-12-3650 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5295     TCGA-12-5299 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-14-0781     TCGA-14-0787     TCGA-14-0789     TCGA-14-0790 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-14-0817     TCGA-14-1823     TCGA-14-1825     TCGA-14-1829 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-14-2554     TCGA-15-0742     TCGA-15-1444     TCGA-16-0846 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-16-1045     TCGA-19-1390     TCGA-19-2619     TCGA-19-2620 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-19-2624     TCGA-19-2625     TCGA-19-2629     TCGA-19-5960 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-26-1442     TCGA-26-5132     TCGA-26-5133     TCGA-26-5134 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-26-5135     TCGA-26-5136     TCGA-26-5139     TCGA-27-1830 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1834     TCGA-27-1835 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-27-1837     TCGA-27-2519     TCGA-27-2521     TCGA-27-2523 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-27-2524     TCGA-27-2526     TCGA-27-2528     TCGA-28-1747 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-1753     TCGA-28-2499     TCGA-28-2509     TCGA-28-2510 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-2513     TCGA-28-2514     TCGA-28-5204     TCGA-28-5207 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-5208     TCGA-28-5209     TCGA-28-5213     TCGA-28-5215 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-5216     TCGA-28-5218     TCGA-28-5220     TCGA-32-1970 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-32-1980     TCGA-32-1982     TCGA-32-2615     TCGA-32-2632 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-32-2634     TCGA-32-2638     TCGA-32-4213     TCGA-32-5222 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-41-2571     TCGA-41-2572     TCGA-41-3915     TCGA-41-4097 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-41-5651     TCGA-76-4925     TCGA-76-4926     TCGA-76-4927 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-76-4928     TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  CD1D MUTATED        0      1      0
  CD1D WILD-TYPE     31     85     24
D30V10, multiclass
[1] "Remove cluster labels:" "CD1D MUTATED"          
clus
  CD1D MUTATED CD1D WILD-TYPE 
             1            140 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0219     TCGA-06-0238 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0644     TCGA-06-0645     TCGA-06-0646     TCGA-06-0649 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0686     TCGA-06-0743     TCGA-06-0744     TCGA-06-0745 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0747     TCGA-06-0749     TCGA-06-0750     TCGA-06-0878 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-0882     TCGA-06-1804     TCGA-06-2557     TCGA-06-2558 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-2559     TCGA-06-2561     TCGA-06-2562     TCGA-06-2563 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-2564     TCGA-06-2565     TCGA-06-2567     TCGA-06-2569 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-2570     TCGA-06-5408     TCGA-06-5410     TCGA-06-5411 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-5412     TCGA-06-5413     TCGA-06-5414     TCGA-06-5415 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-5417     TCGA-06-5418     TCGA-06-5856     TCGA-06-5858 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-06-5859     TCGA-08-0386     TCGA-12-0616     TCGA-12-0618 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-12-0619     TCGA-12-0821     TCGA-12-1597     TCGA-12-3650 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5295     TCGA-12-5299 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-14-0781     TCGA-14-0787     TCGA-14-0789     TCGA-14-0790 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-14-0817     TCGA-14-1823     TCGA-14-1825     TCGA-14-1829 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-14-2554     TCGA-15-0742     TCGA-15-1444     TCGA-16-0846 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-16-1045     TCGA-19-1390     TCGA-19-2619     TCGA-19-2620 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-19-2624     TCGA-19-2625     TCGA-19-2629     TCGA-19-5960 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-26-1442     TCGA-26-5132     TCGA-26-5133     TCGA-26-5134 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-26-5135     TCGA-26-5136     TCGA-26-5139     TCGA-27-1830 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1834     TCGA-27-1835 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-27-1837     TCGA-27-2519     TCGA-27-2521     TCGA-27-2523 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-27-2524     TCGA-27-2526     TCGA-27-2528     TCGA-28-1747 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-1753     TCGA-28-2499     TCGA-28-2509     TCGA-28-2510 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-2513     TCGA-28-2514     TCGA-28-5204     TCGA-28-5207 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-5208     TCGA-28-5209     TCGA-28-5213     TCGA-28-5215 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-28-5216     TCGA-28-5218     TCGA-28-5220     TCGA-32-1970 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-32-1980     TCGA-32-1982     TCGA-32-2615     TCGA-32-2632 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-32-2634     TCGA-32-2638     TCGA-32-4213     TCGA-32-5222 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-41-2571     TCGA-41-2572     TCGA-41-3915     TCGA-41-4097 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-41-5651     TCGA-76-4925     TCGA-76-4926     TCGA-76-4927 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 
    TCGA-76-4928     TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" "CD1D WILD-TYPE" 

Clustering(31) Variable = LZTR1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        2      1      2      2
  LZTR1 WILD-TYPE     67     42     72     52
D31V1, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             2              67
  CLUS_2             1              42
  CLUS_3             2              72
  CLUS_4             2              52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        3      2      0      2
  LZTR1 WILD-TYPE     60     48     48     77
D31V2, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             3              60
  CLUS_2             2              48
  CLUS_3             0              48
  CLUS_4             2              77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        5      3      0      2
  LZTR1 WILD-TYPE     72     90     45     58
D31V3, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             5              72
  CLUS_2             3              90
  CLUS_3             0              45
  CLUS_4             2              58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        4      3      3
  LZTR1 WILD-TYPE    134     58     73
D31V4, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             4             134
  CLUS_2             3              58
  CLUS_3             3              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
  LZTR1 MUTATED        4      4      1
  LZTR1 WILD-TYPE     81    103     80
D31V5, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             4              81
  CLUS_2             4             103
  CLUS_3             1              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        3      2      0
  LZTR1 WILD-TYPE     32     42     29
D31V6, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             3              32
  CLUS_2             2              42
  CLUS_3             0              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LZTR1 MUTATED        1      2      2      2
  LZTR1 WILD-TYPE     40     36     29     31
D31V7, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             2              36
  CLUS_3             2              29
  CLUS_4             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        3      2      2
  LZTR1 WILD-TYPE     45     50     41
D31V8, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             3              45
  CLUS_2             2              50
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        2      0      1
  LZTR1 WILD-TYPE     42     62     34
D31V9, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             2              42
  CLUS_2             0              62
  CLUS_3             1              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LZTR1 MUTATED        0      3      0
  LZTR1 WILD-TYPE     31     83     24
D31V10, multiclass
        clus
vv       LZTR1 MUTATED LZTR1 WILD-TYPE
  CLUS_1             0              31
  CLUS_2             3              83
  CLUS_3             0              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = TEX15 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TEX15 MUTATED        2      1      1      4
  TEX15 WILD-TYPE     67     42     73     50
D32V1, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             2              67
  CLUS_2             1              42
  CLUS_3             1              73
  CLUS_4             4              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TEX15 MUTATED        1      2      0      5
  TEX15 WILD-TYPE     62     48     48     74
D32V2, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             1              62
  CLUS_2             2              48
  CLUS_3             0              48
  CLUS_4             5              74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TEX15 MUTATED        1      5      0      2
  TEX15 WILD-TYPE     76     88     45     58
D32V3, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             1              76
  CLUS_2             5              88
  CLUS_3             0              45
  CLUS_4             2              58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TEX15 MUTATED        3      2      3
  TEX15 WILD-TYPE    135     59     73
D32V4, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             3             135
  CLUS_2             2              59
  CLUS_3             3              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
  TEX15 MUTATED        4      2      2
  TEX15 WILD-TYPE     81    105     79
D32V5, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             4              81
  CLUS_2             2             105
  CLUS_3             2              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TEX15 MUTATED        0      1      2
  TEX15 WILD-TYPE     35     43     27
D32V6, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             0              35
  CLUS_2             1              43
  CLUS_3             2              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TEX15 MUTATED        1      1      1      2
  TEX15 WILD-TYPE     40     37     30     31
D32V7, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             1              37
  CLUS_3             1              30
  CLUS_4             2              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TEX15 MUTATED        0      3      2
  TEX15 WILD-TYPE     48     49     41
D32V8, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             0              48
  CLUS_2             3              49
  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"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TEX15 MUTATED        5      0      0
  TEX15 WILD-TYPE     39     62     35
D32V9, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             5              39
  CLUS_2             0              62
  CLUS_3             0              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  TEX15 MUTATED        1      4      0
  TEX15 WILD-TYPE     30     82     24
D32V10, multiclass
        clus
vv       TEX15 MUTATED TEX15 WILD-TYPE
  CLUS_1             1              30
  CLUS_2             4              82
  CLUS_3             0              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = FBN3 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBN3 MUTATED        1      1      6      1
  FBN3 WILD-TYPE     68     42     68     53
D33V1, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            1             42
  CLUS_3            6             68
  CLUS_4            1             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBN3 MUTATED        1      2      4      2
  FBN3 WILD-TYPE     62     48     44     77
D33V2, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            1             62
  CLUS_2            2             48
  CLUS_3            4             44
  CLUS_4            2             77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBN3 MUTATED        4      3      2      2
  FBN3 WILD-TYPE     73     90     43     58
D33V3, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            4             73
  CLUS_2            3             90
  CLUS_3            2             43
  CLUS_4            2             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FBN3 MUTATED        5      3      3
  FBN3 WILD-TYPE    133     58     73
D33V4, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            5            133
  CLUS_2            3             58
  CLUS_3            3             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
  FBN3 MUTATED        3      7      1
  FBN3 WILD-TYPE     82    100     80
D33V5, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            3             82
  CLUS_2            7            100
  CLUS_3            1             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FBN3 MUTATED        1      3      0
  FBN3 WILD-TYPE     34     41     29
D33V6, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            1             34
  CLUS_2            3             41
  CLUS_3            0             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FBN3 MUTATED        0      3      1      2
  FBN3 WILD-TYPE     41     35     30     31
D33V7, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            3             35
  CLUS_3            1             30
  CLUS_4            2             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FBN3 MUTATED        1      4      1
  FBN3 WILD-TYPE     47     48     42
D33V8, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            1             47
  CLUS_2            4             48
  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"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FBN3 MUTATED        1      3      1
  FBN3 WILD-TYPE     43     59     34
D33V9, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            1             43
  CLUS_2            3             59
  CLUS_3            1             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  FBN3 MUTATED        1      3      1
  FBN3 WILD-TYPE     30     83     23
D33V10, multiclass
        clus
vv       FBN3 MUTATED FBN3 WILD-TYPE
  CLUS_1            1             30
  CLUS_2            3             83
  CLUS_3            1             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
