
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_mutation_onlysig.3.4048/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_mutation_onlysig.3.4048/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/480749/COAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/COAD-TP/4429990/COAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=COAD-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=COAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=436, in cluster file=154, common to both=154
[1]  16 154
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          103            51 
  APC MUTATED APC WILD-TYPE 
          103            51 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              128 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              128 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            20            134 
  BRAF MUTATED BRAF WILD-TYPE 
            20            134 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            58             96 
  KRAS MUTATED KRAS WILD-TYPE 
            58             96 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            74             80 
  TP53 MUTATED TP53 WILD-TYPE 
            74             80 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             125 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             125 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            139 
  NRAS MUTATED NRAS WILD-TYPE 
            15            139 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             136 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             136 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               135 
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               135 
[1] "SOX9 MUTATION ANALYSIS"
[1] 3
  SOX9 MUTATED SOX9 WILD-TYPE 
             9            145 
  SOX9 MUTATED SOX9 WILD-TYPE 
             9            145 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               8              146 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               8              146 
[1] "TNFRSF10C MUTATION ANALYSIS"
[1] 3
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 148 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 148 
[1] "ACOT4 MUTATION ANALYSIS"
[1] 3
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             151 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             151 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             144 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             144 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             150 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             150 
[1] "GGT1 MUTATION ANALYSIS"
[1] 3
  GGT1 MUTATED GGT1 WILD-TYPE 
             3            151 
  GGT1 MUTATED GGT1 WILD-TYPE 
             3            151 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 154 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"            "MRNA_CHIERARCHICAL"   "CN_CNMF"             
[4] "RPPA_CNMF"            "RPPA_CHIERARCHICAL"   "MIRSEQ_CNMF"         
[7] "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 154 columns, 0 survival variables, and 7 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          18            16
  CLUS_2          42            15
  CLUS_3          21             7
  CLUS_4          14             8
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          40            13
  CLUS_2          21            21
  CLUS_3          34            12
D1V3, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          55            17
  CLUS_2          35            29
  CLUS_3          11             5
D1V4, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          19             4
  CLUS_2          28            19
  CLUS_3          12             6
  CLUS_4           9             7
D1V5, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           4             3
  CLUS_2           5             3
  CLUS_3           9             1
  CLUS_4          50            29
D1V6, binary
               cls
clus             0  1
  APC MUTATED    2 92
  APC WILD-TYPE  2 45
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      2   92
  APC WILD-TYPE    2   45
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_2           2             2
  CLUS_3          92            45
D1V7, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           1             1
  CLUS_2          93            45
  CLUS_3           0             1

Clustering(2) Variable = PIK3CA MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               28
  CLUS_2              5               52
  CLUS_3              6               22
  CLUS_4              4               18
D2V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9               44
  CLUS_2              8               34
  CLUS_3              4               42
D2V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               67
  CLUS_2             16               48
  CLUS_3              4               12
D2V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               15
  CLUS_2              8               39
  CLUS_3              1               17
  CLUS_4              4               12
D2V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                6
  CLUS_2              2                6
  CLUS_3              4                6
  CLUS_4             14               65
D2V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  22
  PIK3CA WILD-TYPE   3 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   22
  PIK3CA WILD-TYPE    3  115
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_2              1                3
  CLUS_3             22              115
D2V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                1
  CLUS_2             22              116
  CLUS_3              0                1

Clustering(3) Variable = BRAF MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           14             20
  CLUS_2            1             56
  CLUS_3            3             25
  CLUS_4            0             22
D3V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             52
  CLUS_2           16             26
  CLUS_3            1             45
D3V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             70
  CLUS_2           17             47
  CLUS_3            1             15
D3V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             20
  CLUS_2            4             43
  CLUS_3            3             15
  CLUS_4            1             15
D3V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1              6
  CLUS_2            1              7
  CLUS_3            1              9
  CLUS_4            8             71
D3V6, binary
                cls
clus               0   1
  BRAF MUTATED     1  19
  BRAF WILD-TYPE   3 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1   19
  BRAF WILD-TYPE    3  118
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_2            1              3
  CLUS_3           19            118
D3V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              2
  CLUS_2           20            118
  CLUS_3            0              1

Clustering(4) Variable = KRAS MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             24
  CLUS_2           16             41
  CLUS_3           17             11
  CLUS_4            7             15
D4V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           27             26
  CLUS_2           16             26
  CLUS_3            7             39
D4V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           22             50
  CLUS_2           25             39
  CLUS_3           10              6
D4V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9             14
  CLUS_2           22             25
  CLUS_3            6             12
  CLUS_4            8              8
D4V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3              4
  CLUS_2            2              6
  CLUS_3            5              5
  CLUS_4           35             44
D4V6, binary
                cls
clus              0  1
  KRAS MUTATED    2 50
  KRAS WILD-TYPE  2 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2   50
  KRAS WILD-TYPE    2   87
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_2            2              2
  CLUS_3           50             87
D4V7, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              2
  CLUS_2           51             87
  CLUS_3            1              0

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             22
  CLUS_2           39             18
  CLUS_3            9             19
  CLUS_4           10             12
D5V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           29             24
  CLUS_2           13             29
  CLUS_3           28             18
D5V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           53             19
  CLUS_2           13             51
  CLUS_3            7              9
D5V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             15
  CLUS_2           24             23
  CLUS_3            8             10
  CLUS_4            4             12
D5V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              4
  CLUS_2            1              7
  CLUS_3            4              6
  CLUS_4           36             43
D5V6, binary
                cls
clus              0  1
  TP53 MUTATED    1 68
  TP53 WILD-TYPE  3 69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   68
  TP53 WILD-TYPE    3   69
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_2            1              3
  CLUS_3           68             69
D5V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              1
  CLUS_2           68             70
  CLUS_3            0              1

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            10              24
  CLUS_2             7              50
  CLUS_3             5              23
  CLUS_4             3              19
D6V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             8              45
  CLUS_2            12              30
  CLUS_3             5              41
D6V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             6              66
  CLUS_2            20              44
  CLUS_3             3              13
D6V4, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              19
  CLUS_2             8              39
  CLUS_3             1              17
  CLUS_4             9               7
D6V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             4               4
  CLUS_3             2               8
  CLUS_4            15              64
D6V6, binary
                 cls
clus                0   1
  FBXW7 MUTATED     0  27
  FBXW7 WILD-TYPE   4 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      0   27
  FBXW7 WILD-TYPE    4  110
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_2             0               4
  CLUS_3            27             110
D6V7, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             1               1
  CLUS_2            26             112
  CLUS_3             0               1

Clustering(7) Variable = NRAS MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             34
  CLUS_2            8             49
  CLUS_3            4             24
  CLUS_4            2             20
D7V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            7             46
  CLUS_2            2             40
  CLUS_3            5             41
D7V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            8             64
  CLUS_2            6             58
  CLUS_3            1             15
D7V4, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             22
  CLUS_2            8             39
  CLUS_3            1             17
  CLUS_4            2             14
D7V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              7
  CLUS_2            2              6
  CLUS_3            0             10
  CLUS_4           10             69
D7V6, binary
                cls
clus               0   1
  NRAS MUTATED     0  13
  NRAS WILD-TYPE   4 124
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   13
  NRAS WILD-TYPE    4  124
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_2            0              4
  CLUS_3           13            124
D7V7, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              2
  CLUS_2           13            125
  CLUS_3            0              1

Clustering(8) Variable = SMAD4 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             6              28
  CLUS_2             4              53
  CLUS_3             5              23
  CLUS_4             2              20
D8V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             5              48
  CLUS_2             7              35
  CLUS_3             5              41
D8V3, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             4              68
  CLUS_2            11              53
  CLUS_3             3              13
D8V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             3              20
  CLUS_2             8              39
  CLUS_3             2              16
  CLUS_4             1              15
D8V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2               5
  CLUS_2             0               8
  CLUS_3             1               9
  CLUS_4            11              68
D8V6, binary
                 cls
clus                0   1
  SMAD4 MUTATED     0  17
  SMAD4 WILD-TYPE   4 120
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      0   17
  SMAD4 WILD-TYPE    4  120
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_2             0               4
  CLUS_3            17             120
D8V7, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               2
  CLUS_2            17             121
  CLUS_3             0               1

Clustering(9) Variable = FAM123B MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               8                26
  CLUS_2               6                51
  CLUS_3               4                24
  CLUS_4               1                21
D9V2, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               8                45
  CLUS_2              10                32
  CLUS_3               1                45
D9V3, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               4                68
  CLUS_2              13                51
  CLUS_3               1                15
D9V4, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                21
  CLUS_2               4                43
  CLUS_3               1                17
  CLUS_4               4                12
D9V5, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                 6
  CLUS_3               1                 9
  CLUS_4               8                71
D9V6, binary
                   cls
clus                  0   1
  FAM123B MUTATED     1  17
  FAM123B WILD-TYPE   3 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      1   17
  FAM123B WILD-TYPE    3  120
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_2               1                 3
  CLUS_3              17               120
D9V7, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                 1
  CLUS_2              17               121
  CLUS_3               0                 1

Clustering(10) Variable = SOX9 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            2             32
  CLUS_2            3             54
  CLUS_3            0             28
  CLUS_4            3             19
D10V2, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            2             51
  CLUS_2            1             41
  CLUS_3            5             41
D10V3, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            2             70
  CLUS_2            6             58
  CLUS_3            1             15
D10V4, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0             23
  CLUS_2            3             44
  CLUS_3            0             18
  CLUS_4            2             14
D10V5, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            1              6
  CLUS_2            0              8
  CLUS_3            0             10
  CLUS_4            4             75
D10V6, binary
                cls
clus               0   1
  SOX9 MUTATED     0   9
  SOX9 WILD-TYPE   4 128
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED      0    9
  SOX9 WILD-TYPE    4  128
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_2            0              4
  CLUS_3            9            128
D10V7, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0              2
  CLUS_2            9            129
  CLUS_3            0              1

Clustering(11) Variable = ACVR2A MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              5               29
  CLUS_2              1               56
  CLUS_3              1               27
  CLUS_4              0               22
D11V2, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              2               51
  CLUS_2              4               38
  CLUS_3              1               45
D11V3, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1               71
  CLUS_2              7               57
  CLUS_3              0               16
D11V4, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0               23
  CLUS_2              4               43
  CLUS_3              0               18
  CLUS_4              2               14
D11V5, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0                7
  CLUS_2              1                7
  CLUS_3              0               10
  CLUS_4              5               74
D11V6, binary
                  cls
clus                 0   1
  ACVR2A MUTATED     0   8
  ACVR2A WILD-TYPE   4 129
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      0    8
  ACVR2A WILD-TYPE    4  129
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_2              0                4
  CLUS_3              8              129
D11V7, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1                1
  CLUS_2              7              131
  CLUS_3              0                1

Clustering(12) Variable = TNFRSF10C MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 2                  32
  CLUS_2                 2                  55
  CLUS_3                 0                  28
  CLUS_4                 2                  20
D12V2, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 2                  51
  CLUS_2                 1                  41
  CLUS_3                 3                  43
D12V3, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 5                  67
  CLUS_2                 1                  63
  CLUS_3                 0                  16
D12V4, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 2                  21
  CLUS_2                 2                  45
  CLUS_3                 0                  18
  CLUS_4                 1                  15
D12V5, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 0                   7
  CLUS_2                 0                   8
  CLUS_3                 2                   8
  CLUS_4                 3                  76
D12V6, binary
                     cls
clus                    0   1
  TNFRSF10C MUTATED     0   6
  TNFRSF10C WILD-TYPE   4 131
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF10C MUTATED      0    6
  TNFRSF10C WILD-TYPE    4  131
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_2                 0                   4
  CLUS_3                 6                 131
D12V7, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 0                   2
  CLUS_2                 6                 132
  CLUS_3                 0                   1

Clustering(13) Variable = ACOT4 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             1              33
  CLUS_2             1              56
  CLUS_3             0              28
  CLUS_4             1              21
D13V2, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             1              52
  CLUS_2             2              40
  CLUS_3             0              46
D13V3, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             1              71
  CLUS_2             1              63
  CLUS_3             1              15
D13V4, multiclass
[1] "Remove cluster labels:" "ACOT4 MUTATED"         
clus
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              1             103 
     TCGA-A6-2672      TCGA-A6-2676      TCGA-A6-2677      TCGA-A6-2678 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3519      TCGA-AA-3520 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3525      TCGA-AA-3529 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3664      TCGA-AA-3672      TCGA-AA-3678 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3688      TCGA-AA-3695      TCGA-AA-3696 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3831 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3844      TCGA-AA-3845 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3852      TCGA-AA-3854 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3872 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3971 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3982 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-A004      TCGA-AA-A00A 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00Q      TCGA-AA-A00R 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01I 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
D13V5, multiclass
[1] "Remove cluster labels:" "ACOT4 MUTATED"         
clus
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              1             103 
     TCGA-A6-2672      TCGA-A6-2676      TCGA-A6-2677      TCGA-A6-2678 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3519      TCGA-AA-3520 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3525      TCGA-AA-3529 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3664      TCGA-AA-3672      TCGA-AA-3678 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3688      TCGA-AA-3695      TCGA-AA-3696 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3831 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3844      TCGA-AA-3845 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3852      TCGA-AA-3854 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3872 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3971 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3982 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-A004      TCGA-AA-A00A 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00Q      TCGA-AA-A00R 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01I 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
D13V6, binary
                 cls
clus                0   1
  ACOT4 MUTATED     0   3
  ACOT4 WILD-TYPE   4 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT4 MUTATED      0    3
  ACOT4 WILD-TYPE    4  134
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             3             134
D13V7, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             0               2
  CLUS_2             3             135
  CLUS_3             0               1

Clustering(14) Variable = SMAD2 MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             3              31
  CLUS_2             1              56
  CLUS_3             4              24
  CLUS_4             1              21
D14V2, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             3              50
  CLUS_2             5              37
  CLUS_3             1              45
D14V3, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             1              71
  CLUS_2             7              57
  CLUS_3             2              14
D14V4, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             2              21
  CLUS_2             3              44
  CLUS_3             1              17
  CLUS_4             1              15
D14V5, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             1               7
  CLUS_3             0              10
  CLUS_4             5              74
D14V6, binary
                 cls
clus                0   1
  SMAD2 MUTATED     0   9
  SMAD2 WILD-TYPE   4 128
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      0    9
  SMAD2 WILD-TYPE    4  128
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             9             128
D14V7, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               2
  CLUS_2             9             129
  CLUS_3             0               1

Clustering(15) Variable = PCBP1 MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              34
  CLUS_2             2              55
  CLUS_3             2              26
  CLUS_4             0              22
D15V2, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             2              51
  CLUS_2             0              42
  CLUS_3             2              44
D15V3, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             2              70
  CLUS_2             1              63
  CLUS_3             1              15
D15V4, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2             102 
     TCGA-A6-2672      TCGA-A6-2676      TCGA-A6-2677      TCGA-A6-2678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3519      TCGA-AA-3520 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3525      TCGA-AA-3529 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3664      TCGA-AA-3672      TCGA-AA-3678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3688      TCGA-AA-3695      TCGA-AA-3696 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3831      TCGA-AA-3833 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3848 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3971 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3982 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00Q      TCGA-AA-A00R 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A022 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
D15V5, multiclass
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2             102 
     TCGA-A6-2672      TCGA-A6-2676      TCGA-A6-2677      TCGA-A6-2678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808      TCGA-A6-3810 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3519      TCGA-AA-3520 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3525      TCGA-AA-3529 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3664      TCGA-AA-3672      TCGA-AA-3678 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3688      TCGA-AA-3695      TCGA-AA-3696 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3831      TCGA-AA-3833 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3848 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3869      TCGA-AA-3872 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3947      TCGA-AA-3955      TCGA-AA-3971 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3982 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00Q      TCGA-AA-A00R 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A022 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
D15V6, binary
                 cls
clus                0   1
  PCBP1 MUTATED     0   3
  PCBP1 WILD-TYPE   4 134
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      0    3
  PCBP1 WILD-TYPE    4  134
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_2             0               4
  CLUS_3             3             134
D15V7, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0               2
  CLUS_2             3             135
  CLUS_3             0               1

Clustering(16) Variable = GGT1 MUTATION ANALYSIS
D16V1, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            139 
    TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2677 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-A6-3810     TCGA-AA-3514     TCGA-AA-3516     TCGA-AA-3517 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3696 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860     TCGA-AA-3864 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3866     TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3977     TCGA-AA-3979     TCGA-AA-3980 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3982     TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01Q     TCGA-AA-A024 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AY-4070     TCGA-AY-4071 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            139 
    TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676     TCGA-A6-2677 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-A6-3810     TCGA-AA-3514     TCGA-AA-3516     TCGA-AA-3517 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3696 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860     TCGA-AA-3864 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3866     TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3977     TCGA-AA-3979     TCGA-AA-3980 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3982     TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01Q     TCGA-AA-A024 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AY-4070     TCGA-AY-4071 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D16V3, multiclass
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  CLUS_1            0             72
  CLUS_2            3             61
  CLUS_3            0             16
D16V4, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            102 
    TCGA-A6-2672     TCGA-A6-2676     TCGA-A6-2677     TCGA-A6-2678 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3810 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3519     TCGA-AA-3520 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3521     TCGA-AA-3522     TCGA-AA-3525     TCGA-AA-3529 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532     TCGA-AA-3534 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3664     TCGA-AA-3672     TCGA-AA-3678 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3688     TCGA-AA-3695     TCGA-AA-3696 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3831 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3844     TCGA-AA-3848 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3856 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3930     TCGA-AA-3947     TCGA-AA-3955     TCGA-AA-3971 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3982 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-A004     TCGA-AA-A00A 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00Q     TCGA-AA-A00R 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01I 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01X     TCGA-AA-A022 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D16V5, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            102 
    TCGA-A6-2672     TCGA-A6-2676     TCGA-A6-2677     TCGA-A6-2678 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808     TCGA-A6-3810 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3519     TCGA-AA-3520 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3521     TCGA-AA-3522     TCGA-AA-3525     TCGA-AA-3529 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532     TCGA-AA-3534 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3664     TCGA-AA-3672     TCGA-AA-3678 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3688     TCGA-AA-3695     TCGA-AA-3696 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3831 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3844     TCGA-AA-3848 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3856 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3869     TCGA-AA-3872 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3930     TCGA-AA-3947     TCGA-AA-3955     TCGA-AA-3971 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3982 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-A004     TCGA-AA-A00A 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00Q     TCGA-AA-A00R 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01I 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01X     TCGA-AA-A022 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D16V6, binary
                cls
clus               0   1
  GGT1 MUTATED     0   3
  GGT1 WILD-TYPE   4 134
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      0    3
  GGT1 WILD-TYPE    4  134
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  CLUS_2            0              4
  CLUS_3            3            134
D16V7, multiclass
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  CLUS_1            0              2
  CLUS_2            3            135
  CLUS_3            0              1
                    V1                     V2                     V3 
           "MRNA_CNMF"   "MRNA_CHIERARCHICAL"              "CN_CNMF" 
                    V4                     V5                     V6 
           "RPPA_CNMF"   "RPPA_CHIERARCHICAL"          "MIRSEQ_CNMF" 
                    V7 
"MIRSEQ_CHIERARCHICAL" 
> q(save="no")
