
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/423557/COADREAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/COADREAD-TP/3537691/COADREAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=COADREAD-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=COADREAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=591, in cluster file=224, common to both=224
[1]  21 224
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          160            64 
  APC MUTATED APC WILD-TYPE 
          160            64 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             186 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             186 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            20            204 
  NRAS MUTATED NRAS WILD-TYPE 
            20            204 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            22            202 
  BRAF MUTATED BRAF WILD-TYPE 
            22            202 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            96            128 
  KRAS MUTATED KRAS WILD-TYPE 
            96            128 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           120            104 
  TP53 MUTATED TP53 WILD-TYPE 
           120            104 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             198 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             198 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               25               199 
  FAM123B MUTATED FAM123B WILD-TYPE 
               25               199 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              33              191 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              33              191 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             209 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             209 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              18              206 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              18              206 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               9              215 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               9              215 
[1] "SOX9 MUTATION ANALYSIS"
[1] 3
  SOX9 MUTATED SOX9 WILD-TYPE 
            10            214 
  SOX9 MUTATED SOX9 WILD-TYPE 
            10            214 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
             6            218 
  ELF3 MUTATED ELF3 WILD-TYPE 
             6            218 
[1] "CRTC1 MUTATION ANALYSIS"
[1] 3
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              6             218 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              6             218 
[1] "TNFRSF10C MUTATION ANALYSIS"
[1] 3
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 218 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 218 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                220 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                220 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                15                209 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                15                209 
[1] "ACOT4 MUTATION ANALYSIS"
[1] 3
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             221 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             221 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            217 
  PTEN MUTATED PTEN WILD-TYPE 
             7            217 
[1] "MYO1B MUTATION ANALYSIS"
[1] 3
  MYO1B MUTATED MYO1B WILD-TYPE 
             13             211 
  MYO1B MUTATED MYO1B WILD-TYPE 
             13             211 
[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 224 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:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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=3,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"            "MRNA_CHIERARCHICAL"   "CN_CNMF"             
[4] "METHLYATION_CNMF"     "RPPA_CNMF"            "RPPA_CHIERARCHICAL"  
[7] "MIRSEQ_CNMF"          "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 224 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_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          21            21
  CLUS_2          46            11
  CLUS_3          50            17
  CLUS_4          30             9
D1V2, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          32             8
  CLUS_2          35            13
  CLUS_3          35            26
  CLUS_4          45            11
D1V3, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          65            21
  CLUS_2          52            31
  CLUS_3          28             8
  CLUS_4          12             4
D1V4, multiclass
[1] "Remove cluster labels:" "APC WILD-TYPE"         
clus
  APC MUTATED APC WILD-TYPE 
            6             1 
 TCGA-AG-A01W  TCGA-AG-A01Y  TCGA-AG-A020  TCGA-AG-A026  TCGA-AG-A02N 
"APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" "APC MUTATED" 
 TCGA-AG-A036 
"APC MUTATED" 
D1V5, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          34            10
  CLUS_2          47            24
  CLUS_3          14             6
  CLUS_4          16             6
D1V6, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          16             4
  CLUS_2          75            34
  CLUS_3          15             4
  CLUS_4           5             4
D1V7, binary
               cls
clus              0   1
  APC MUTATED   144   5
  APC WILD-TYPE  55   3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    144    5
  APC WILD-TYPE   55    3
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1         144            55
  CLUS_3           5             3
D1V8, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1         135            55
  CLUS_2           9             1
  CLUS_3           5             2

Clustering(2) Variable = FBXW7 MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            11              31
  CLUS_2             6              51
  CLUS_3             7              60
  CLUS_4             9              30
D2V2, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              36
  CLUS_2             5              43
  CLUS_3            17              44
  CLUS_4             7              49
D2V3, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             4              82
  CLUS_2            24              59
  CLUS_3             8              28
  CLUS_4             2              14
D2V4, multiclass
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2               5 
     TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A036 
"FBXW7 WILD-TYPE" 
D2V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             8              36
  CLUS_2             9              62
  CLUS_3             2              18
  CLUS_4            10              12
D2V6, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             3              17
  CLUS_2            18              91
  CLUS_3             8              11
  CLUS_4             0               9
D2V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED    36   0
  FBXW7 WILD-TYPE 163   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     36    0
  FBXW7 WILD-TYPE  163    8
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            36             163
  CLUS_3             0               8
D2V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1            31             159
  CLUS_2             4               6
  CLUS_3             1               6

Clustering(3) Variable = NRAS MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             42
  CLUS_2            8             49
  CLUS_3            6             61
  CLUS_4            5             34
D3V2, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1             39
  CLUS_2            8             40
  CLUS_3            4             57
  CLUS_4            6             50
D3V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            9             77
  CLUS_2           10             73
  CLUS_3            1             35
  CLUS_4            0             16
D3V4, multiclass
D3V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            2             42
  CLUS_2            9             62
  CLUS_3            0             20
  CLUS_4            2             20
D3V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0             20
  CLUS_2           10             99
  CLUS_3            2             17
  CLUS_4            1              8
D3V7, binary
                cls
clus               0   1
  NRAS MUTATED    18   0
  NRAS WILD-TYPE 181   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     18    0
  NRAS WILD-TYPE  181    8
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           18            181
  CLUS_3            0              8
D3V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1           17            173
  CLUS_2            1              9
  CLUS_3            0              7

Clustering(4) Variable = BRAF MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           13             29
  CLUS_2            1             56
  CLUS_3            1             66
  CLUS_4            5             34
D4V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             39
  CLUS_2            0             48
  CLUS_3           18             43
  CLUS_4            1             55
D4V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             85
  CLUS_2           18             65
  CLUS_3            3             33
  CLUS_4            0             16
D4V4, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1              6 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A036 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 
D4V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             41
  CLUS_2            4             67
  CLUS_3            4             16
  CLUS_4            2             20
D4V6, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             19
  CLUS_2            8            101
  CLUS_3            2             17
  CLUS_4            2              7
D4V7, binary
                cls
clus               0   1
  BRAF MUTATED    21   1
  BRAF WILD-TYPE 178   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     21    1
  BRAF WILD-TYPE  178    7
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           21            178
  CLUS_3            1              7
D4V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1           21            169
  CLUS_2            1              9
  CLUS_3            0              7

Clustering(5) Variable = KRAS MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           13             29
  CLUS_2           14             43
  CLUS_3           31             36
  CLUS_4           27             12
D5V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             30
  CLUS_2           33             15
  CLUS_3           26             35
  CLUS_4           16             40
D5V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           32             54
  CLUS_2           40             43
  CLUS_3           15             21
  CLUS_4            8              8
D5V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              2
  CLUS_2            3              1
  CLUS_3            0              1
D5V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           19             25
  CLUS_2           36             35
  CLUS_3            7             13
  CLUS_4           10             12
D5V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            9             11
  CLUS_2           50             59
  CLUS_3            9             10
  CLUS_4            4              5
D5V7, binary
                cls
clus               0   1
  KRAS MUTATED    80   6
  KRAS WILD-TYPE 119   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     80    6
  KRAS WILD-TYPE  119    2
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           80            119
  CLUS_3            6              2
D5V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           79            111
  CLUS_2            5              5
  CLUS_3            2              5

Clustering(6) Variable = TP53 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           17             25
  CLUS_2           40             17
  CLUS_3           39             28
  CLUS_4           14             25
D6V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           30             10
  CLUS_2           19             29
  CLUS_3           25             36
  CLUS_4           36             20
D6V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           68             18
  CLUS_2           22             61
  CLUS_3           19             17
  CLUS_4            9              7
D6V4, multiclass
[1] "Remove cluster labels:" "TP53 WILD-TYPE"        
clus
  TP53 MUTATED TP53 WILD-TYPE 
             6              1 
  TCGA-AG-A01W   TCGA-AG-A01Y   TCGA-AG-A020   TCGA-AG-A026   TCGA-AG-A02N 
"TP53 MUTATED" "TP53 MUTATED" "TP53 MUTATED" "TP53 MUTATED" "TP53 MUTATED" 
  TCGA-AG-A036 
"TP53 MUTATED" 
D6V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           19             25
  CLUS_2           36             35
  CLUS_3           13              7
  CLUS_4           11             11
D6V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             12
  CLUS_2           57             52
  CLUS_3            9             10
  CLUS_4            5              4
D6V7, binary
                cls
clus               0   1
  TP53 MUTATED   111   1
  TP53 WILD-TYPE  88   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    111    1
  TP53 WILD-TYPE   88    7
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1          111             88
  CLUS_3            1              7
D6V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           99             91
  CLUS_2            7              3
  CLUS_3            6              1

Clustering(7) Variable = SMAD4 MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             7              35
  CLUS_2             4              53
  CLUS_3             4              63
  CLUS_4             9              30
D7V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             5              35
  CLUS_2             6              42
  CLUS_3            10              51
  CLUS_4             3              53
D7V3, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             4              82
  CLUS_2            15              68
  CLUS_3             5              31
  CLUS_4             2              14
D7V4, multiclass
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1               6 
     TCGA-A6-2672      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A026 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A036 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
D7V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             6              38
  CLUS_2            10              61
  CLUS_3             4              16
  CLUS_4             1              21
D7V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              18
  CLUS_2            14              95
  CLUS_3             2              17
  CLUS_4             3               6
D7V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED    24   1
  SMAD4 WILD-TYPE 175   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     24    1
  SMAD4 WILD-TYPE  175    7
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1            24             175
  CLUS_3             1               7
D7V8, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1            24             166
  CLUS_2             1               9
  CLUS_3             0               7

Clustering(8) Variable = FAM123B MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               9                33
  CLUS_2               5                52
  CLUS_3               4                63
  CLUS_4               6                33
D8V2, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                38
  CLUS_2               3                45
  CLUS_3              12                49
  CLUS_4               7                49
D8V3, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               6                80
  CLUS_2              17                66
  CLUS_3               1                35
  CLUS_4               0                16
D8V4, multiclass
[1] "Remove cluster labels:" "FAM123B MUTATED"       
clus
  FAM123B MUTATED FAM123B WILD-TYPE 
                1                 6 
       TCGA-A6-2672        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A036 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
D8V5, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               3                41
  CLUS_2               7                64
  CLUS_3               2                18
  CLUS_4               4                18
D8V6, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                19
  CLUS_2              12                97
  CLUS_3               3                16
  CLUS_4               0                 9
D8V7, binary
                   cls
clus                  0   1
  FAM123B MUTATED    23   1
  FAM123B WILD-TYPE 176   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     23    1
  FAM123B WILD-TYPE  176    7
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1              23               176
  CLUS_3               1                 7
D8V8, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1              22               168
  CLUS_2               2                 8
  CLUS_3               0                 7

Clustering(9) Variable = PIK3CA MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               34
  CLUS_2              4               53
  CLUS_3              7               60
  CLUS_4              7               32
D9V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               37
  CLUS_2              7               41
  CLUS_3             10               51
  CLUS_4              6               50
D9V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               81
  CLUS_2             22               61
  CLUS_3              2               34
  CLUS_4              3               13
D9V4, multiclass
[1] "Remove cluster labels:" "PIK3CA MUTATED"        
clus
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               2                5 
      TCGA-A6-2672       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A026 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A036 
"PIK3CA WILD-TYPE" 
D9V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               33
  CLUS_2              9               62
  CLUS_3              1               19
  CLUS_4              6               16
D9V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               14
  CLUS_2             16               93
  CLUS_3              5               14
  CLUS_4              0                9
D9V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    26   3
  PIK3CA WILD-TYPE 173   5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     26    3
  PIK3CA WILD-TYPE  173    5
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             26              173
  CLUS_3              3                5
D9V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             27              163
  CLUS_2              1                9
  CLUS_3              1                6

Clustering(10) Variable = SMAD2 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             4              38
  CLUS_2             2              55
  CLUS_3             2              65
  CLUS_4             5              34
D10V2, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             3              37
  CLUS_2             2              46
  CLUS_3             6              55
  CLUS_4             2              54
D10V3, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             4              82
  CLUS_2             8              75
  CLUS_3             0              36
  CLUS_4             3              13
D10V4, multiclass
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              1               6 
     TCGA-A6-2672      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A026 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A036 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
D10V5, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             2              42
  CLUS_2             4              67
  CLUS_3             1              19
  CLUS_4             3              19
D10V6, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             6             103
  CLUS_3             3              16
  CLUS_4             1               8
D10V7, binary
                 cls
clus                0   1
  SMAD2 MUTATED    14   0
  SMAD2 WILD-TYPE 185   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     14    0
  SMAD2 WILD-TYPE  185    8
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1            14             185
  CLUS_3             0               8
D10V8, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1            13             177
  CLUS_2             1               9
  CLUS_3             0               7

Clustering(11) Variable = TCF7L2 MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              3               39
  CLUS_2              4               53
  CLUS_3              5               62
  CLUS_4              3               36
D11V2, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              4               36
  CLUS_2              5               43
  CLUS_3              2               59
  CLUS_4              4               52
D11V3, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              7               79
  CLUS_2              6               77
  CLUS_3              2               34
  CLUS_4              3               13
D11V4, multiclass
D11V5, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              3               41
  CLUS_2              5               66
  CLUS_3              1               19
  CLUS_4              3               19
D11V6, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              1               19
  CLUS_2              9              100
  CLUS_3              2               17
  CLUS_4              0                9
D11V7, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    15   0
  TCF7L2 WILD-TYPE 184   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     15    0
  TCF7L2 WILD-TYPE  184    8
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1             15              184
  CLUS_3              0                8
D11V8, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1             13              177
  CLUS_2              2                8
  CLUS_3              0                7

Clustering(12) Variable = ACVR2A MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              5               37
  CLUS_2              1               56
  CLUS_3              0               67
  CLUS_4              2               37
D12V2, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1               39
  CLUS_2              0               48
  CLUS_3              5               56
  CLUS_4              2               54
D12V3, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1               85
  CLUS_2              8               75
  CLUS_3              0               36
  CLUS_4              0               16
D12V4, multiclass
[1] "Remove cluster labels:" "ACVR2A MUTATED"        
clus
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               1                6 
      TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A026 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A036 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
D12V5, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1               43
  CLUS_2              4               67
  CLUS_3              0               20
  CLUS_4              2               20
D12V6, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0               20
  CLUS_2              5              104
  CLUS_3              2               17
  CLUS_4              0                9
D12V7, binary
                  cls
clus                 0   1
  ACVR2A MUTATED     9   0
  ACVR2A WILD-TYPE 190   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      9    0
  ACVR2A WILD-TYPE  190    8
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              9              190
  CLUS_3              0                8
D12V8, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              8              182
  CLUS_2              1                9
  CLUS_3              0                7

Clustering(13) Variable = SOX9 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            2             40
  CLUS_2            1             56
  CLUS_3            6             61
  CLUS_4            0             39
D13V2, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            2             38
  CLUS_2            5             43
  CLUS_3            1             60
  CLUS_4            1             55
D13V3, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0             86
  CLUS_2            9             74
  CLUS_3            1             35
  CLUS_4            0             16
D13V4, multiclass
D13V5, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0             44
  CLUS_2            3             68
  CLUS_3            0             20
  CLUS_4            2             20
D13V6, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            4            105
  CLUS_3            1             18
  CLUS_4            0              9
D13V7, binary
                cls
clus               0   1
  SOX9 MUTATED    10   0
  SOX9 WILD-TYPE 189   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     10    0
  SOX9 WILD-TYPE  189    8
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1           10            189
  CLUS_3            0              8
D13V8, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            9            181
  CLUS_2            1              9
  CLUS_3            0              7

Clustering(14) Variable = ELF3 MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             41
  CLUS_2            0             57
  CLUS_3            3             64
  CLUS_4            2             37
D14V2, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             38
  CLUS_2            1             47
  CLUS_3            2             59
  CLUS_4            1             55
D14V3, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             86
  CLUS_2            3             80
  CLUS_3            3             33
  CLUS_4            0             16
D14V4, multiclass
D14V5, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             42
  CLUS_2            1             70
  CLUS_3            0             20
  CLUS_4            1             21
D14V6, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             19
  CLUS_2            2            107
  CLUS_3            1             18
  CLUS_4            0              9
D14V7, binary
                cls
clus               0   1
  ELF3 MUTATED     6   0
  ELF3 WILD-TYPE 193   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      6    0
  ELF3 WILD-TYPE  193    8
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            6            193
  CLUS_3            0              8
D14V8, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            5            185
  CLUS_2            1              9
  CLUS_3            0              7

Clustering(15) Variable = CRTC1 MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             0              57
  CLUS_3             4              63
  CLUS_4             0              39
D15V2, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             3              37
  CLUS_2             1              47
  CLUS_3             2              59
  CLUS_4             0              56
D15V3, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             3              83
  CLUS_2             3              80
  CLUS_3             0              36
  CLUS_4             0              16
D15V4, multiclass
D15V5, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             2              42
  CLUS_2             0              71
  CLUS_3             0              20
  CLUS_4             1              21
D15V6, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             2             107
  CLUS_3             1              18
  CLUS_4             0               9
D15V7, binary
                 cls
clus                0   1
  CRTC1 MUTATED     6   0
  CRTC1 WILD-TYPE 193   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      6    0
  CRTC1 WILD-TYPE  193    8
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             6             193
  CLUS_3             0               8
D15V8, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             5             185
  CLUS_2             1               9
  CLUS_3             0               7

Clustering(16) Variable = TNFRSF10C MUTATION ANALYSIS
D16V1, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 3                  39
  CLUS_2                 1                  56
  CLUS_3                 2                  65
  CLUS_4                 0                  39
D16V2, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 1                  39
  CLUS_2                 3                  45
  CLUS_3                 2                  59
  CLUS_4                 0                  56
D16V3, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 2                  84
  CLUS_2                 2                  81
  CLUS_3                 1                  35
  CLUS_4                 1                  15
D16V4, multiclass
D16V5, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 2                  42
  CLUS_2                 2                  69
  CLUS_3                 0                  20
  CLUS_4                 1                  21
D16V6, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 2                  18
  CLUS_2                 3                 106
  CLUS_3                 0                  19
  CLUS_4                 0                   9
D16V7, binary
                     cls
clus                    0   1
  TNFRSF10C MUTATED     6   0
  TNFRSF10C WILD-TYPE 193   8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF10C MUTATED      6    0
  TNFRSF10C WILD-TYPE  193    8
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 6                 193
  CLUS_3                 0                   8
D16V8, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 6                 184
  CLUS_2                 0                  10
  CLUS_3                 0                   7

Clustering(17) Variable = KRTAP5-5 MUTATION ANALYSIS
D17V1, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 41
  CLUS_2                0                 57
  CLUS_3                3                 64
  CLUS_4                0                 39
D17V2, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                1                 39
  CLUS_2                2                 46
  CLUS_3                1                 60
  CLUS_4                0                 56
D17V3, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                2                 84
  CLUS_2                1                 82
  CLUS_3                0                 36
  CLUS_4                1                 15
D17V4, multiclass
D17V5, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                3                 68
  CLUS_3                1                 19
  CLUS_4                0                 22
D17V6, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                4                105
  CLUS_3                0                 19
  CLUS_4                0                  9
D17V7, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     3   0
  KRTAP5-5 WILD-TYPE 196   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      3    0
  KRTAP5-5 WILD-TYPE  196    8
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                196
  CLUS_3                0                  8
D17V8, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                3                187
  CLUS_2                0                 10
  CLUS_3                0                  7

Clustering(18) Variable = KIAA1804 MUTATION ANALYSIS
D18V1, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                1                 56
  CLUS_3                6                 61
  CLUS_4                4                 35
D18V2, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                4                 36
  CLUS_2                2                 46
  CLUS_3                6                 55
  CLUS_4                2                 54
D18V3, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                4                 82
  CLUS_2               10                 73
  CLUS_3                0                 36
  CLUS_4                1                 15
D18V4, multiclass
[1] "Remove cluster labels:" "KIAA1804 MUTATED"      
clus
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 1                  6 
        TCGA-A6-2672         TCGA-AG-A01W         TCGA-AG-A01Y 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A026         TCGA-AG-A036 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
D18V5, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 41
  CLUS_2                6                 65
  CLUS_3                1                 19
  CLUS_4                3                 19
D18V6, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                 20
  CLUS_2               11                 98
  CLUS_3                2                 17
  CLUS_4                0                  9
D18V7, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    15   0
  KIAA1804 WILD-TYPE 184   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     15    0
  KIAA1804 WILD-TYPE  184    8
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1               15                184
  CLUS_3                0                  8
D18V8, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1               14                176
  CLUS_2                1                  9
  CLUS_3                0                  7

Clustering(19) Variable = ACOT4 MUTATION ANALYSIS
D19V1, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             0              57
  CLUS_3             1              66
  CLUS_4             0              39
D19V2, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             0              40
  CLUS_2             1              47
  CLUS_3             2              59
  CLUS_4             0              56
D19V3, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             1              85
  CLUS_2             2              81
  CLUS_3             0              36
  CLUS_4             0              16
D19V4, multiclass
D19V5, multiclass
[1] "Remove cluster labels:" "ACOT4 MUTATED"         
clus
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              1             156 
     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      TCGA-AF-2689 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3578 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3609 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3612      TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3882      TCGA-AG-3893      TCGA-AG-3896      TCGA-AG-3898 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-4001      TCGA-AG-4005 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A026 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A036 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
D19V6, multiclass
[1] "Remove cluster labels:" "ACOT4 MUTATED"         
clus
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              1             156 
     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      TCGA-AF-2689 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AG-3574      TCGA-AG-3578 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3609 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3612      TCGA-AG-3727      TCGA-AG-3878      TCGA-AG-3881 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3882      TCGA-AG-3893      TCGA-AG-3896      TCGA-AG-3898 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-4001      TCGA-AG-4005 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A026 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A036 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
D19V7, binary
                 cls
clus                0   1
  ACOT4 MUTATED     3   0
  ACOT4 WILD-TYPE 196   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT4 MUTATED      3    0
  ACOT4 WILD-TYPE  196    8
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             3             196
  CLUS_3             0               8
D19V8, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             3             187
  CLUS_2             0              10
  CLUS_3             0               7

Clustering(20) Variable = PTEN MUTATION ANALYSIS
D20V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             40
  CLUS_2            0             57
  CLUS_3            1             66
  CLUS_4            4             35
D20V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             39
  CLUS_2            0             48
  CLUS_3            4             57
  CLUS_4            2             54
D20V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             86
  CLUS_2            6             77
  CLUS_3            1             35
  CLUS_4            0             16
D20V4, multiclass
D20V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             42
  CLUS_2            1             70
  CLUS_3            0             20
  CLUS_4            1             21
D20V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             19
  CLUS_2            2            107
  CLUS_3            1             18
  CLUS_4            0              9
D20V7, binary
                cls
clus               0   1
  PTEN MUTATED     6   1
  PTEN WILD-TYPE 193   7
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      6    1
  PTEN WILD-TYPE  193    7
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6            193
  CLUS_3            1              7
D20V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5            185
  CLUS_2            2              8
  CLUS_3            0              7

Clustering(21) Variable = MYO1B MUTATION ANALYSIS
D21V1, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             6              36
  CLUS_2             1              56
  CLUS_3             1              66
  CLUS_4             4              35
D21V2, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             3              37
  CLUS_2             0              48
  CLUS_3             8              53
  CLUS_4             1              55
D21V3, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             2              84
  CLUS_2            11              72
  CLUS_3             0              36
  CLUS_4             0              16
D21V4, multiclass
[1] "Remove cluster labels:" "MYO1B MUTATED"         
clus
  MYO1B MUTATED MYO1B WILD-TYPE 
              1               6 
     TCGA-A6-2672      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"MYO1B WILD-TYPE" "MYO1B WILD-TYPE" "MYO1B WILD-TYPE" "MYO1B WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A036 
"MYO1B WILD-TYPE" "MYO1B WILD-TYPE" 
D21V5, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             3              41
  CLUS_2             0              71
  CLUS_3             1              19
  CLUS_4             3              19
D21V6, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             0              20
  CLUS_2             5             104
  CLUS_3             2              17
  CLUS_4             0               9
D21V7, binary
                 cls
clus                0   1
  MYO1B MUTATED    12   0
  MYO1B WILD-TYPE 187   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1B MUTATED     12    0
  MYO1B WILD-TYPE  187    8
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1            12             187
  CLUS_3             0               8
D21V8, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1            11             179
  CLUS_2             1               9
  CLUS_3             0               7
                    V1                     V2                     V3 
           "MRNA_CNMF"   "MRNA_CHIERARCHICAL"              "CN_CNMF" 
                    V4                     V5                     V6 
    "METHLYATION_CNMF"            "RPPA_CNMF"   "RPPA_CHIERARCHICAL" 
                    V7                     V8 
         "MIRSEQ_CNMF" "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
