
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/480779/COADREAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/COADREAD-TP/4432153/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=602, in cluster file=223, common to both=223
[1]  24 223
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          160            63 
  APC MUTATED APC WILD-TYPE 
          160            63 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             185 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             38             185 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            20            203 
  NRAS MUTATED NRAS WILD-TYPE 
            20            203 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            22            201 
  BRAF MUTATED BRAF WILD-TYPE 
            22            201 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            96            127 
  KRAS MUTATED KRAS WILD-TYPE 
            96            127 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           119            104 
  TP53 MUTATED TP53 WILD-TYPE 
           119            104 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             197 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             26             197 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               25               198 
  FAM123B MUTATED FAM123B WILD-TYPE 
               25               198 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              33              190 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              33              190 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             208 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             15             208 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              18              205 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              18              205 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               9              214 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               9              214 
[1] "SOX9 MUTATION ANALYSIS"
[1] 3
  SOX9 MUTATED SOX9 WILD-TYPE 
            10            213 
  SOX9 MUTATED SOX9 WILD-TYPE 
            10            213 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
             6            217 
  ELF3 MUTATED ELF3 WILD-TYPE 
             6            217 
[1] "CRTC1 MUTATION ANALYSIS"
[1] 3
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              6             217 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              6             217 
[1] "TNFRSF10C MUTATION ANALYSIS"
[1] 3
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 217 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 217 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                15                208 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                15                208 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                219 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 4                219 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            216 
  PTEN MUTATED PTEN WILD-TYPE 
             7            216 
[1] "ACOT4 MUTATION ANALYSIS"
[1] 3
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             220 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             220 
[1] "MYO1B MUTATION ANALYSIS"
[1] 3
  MYO1B MUTATED MYO1B WILD-TYPE 
             13             210 
  MYO1B MUTATED MYO1B WILD-TYPE 
             13             210 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              6             217 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              6             217 
[1] "GGT1 MUTATION ANALYSIS"
[1] 3
  GGT1 MUTATED GGT1 WILD-TYPE 
             3            220 
  GGT1 MUTATED GGT1 WILD-TYPE 
             3            220 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              14              209 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              14              209 
[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 223 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=3,	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] "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 223 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=3, 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          59            18
  CLUS_2          50            32
  CLUS_3          44            12
  CLUS_4           4             1
D1V4, multiclass
D1V5, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1          32             8
  CLUS_2          44            23
  CLUS_3          17             7
  CLUS_4          18             8
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, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           3             0
  CLUS_2           5             4
  CLUS_3         141            53
D1V8, multiclass
        clus
vv       APC MUTATED APC WILD-TYPE
  CLUS_1           6             2
  CLUS_2           1             1
  CLUS_3         142            54

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              73
  CLUS_2            24              58
  CLUS_3             9              47
  CLUS_4             1               4
D2V4, multiclass
[1] "Remove cluster labels:" "FBXW7 MUTATED"         
clus
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2               6 
     TCGA-A6-3810      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A036 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
D2V5, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             7              33
  CLUS_2             9              58
  CLUS_3             2              22
  CLUS_4            11              15
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, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               3
  CLUS_2             0               9
  CLUS_3            36             158
D2V8, multiclass
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1               1
  CLUS_3            35             161

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           10             67
  CLUS_2            9             73
  CLUS_3            1             55
  CLUS_4            0              5
D3V4, multiclass
D3V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             37
  CLUS_2            7             60
  CLUS_3            1             23
  CLUS_4            2             24
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, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            1              2
  CLUS_2            0              9
  CLUS_3           17            177
D3V8, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            0              8
  CLUS_2            0              2
  CLUS_3           18            178

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             76
  CLUS_2           18             64
  CLUS_3            3             53
  CLUS_4            0              5
D4V4, multiclass
D4V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            3             37
  CLUS_2            4             63
  CLUS_3            4             20
  CLUS_4            2             24
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, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              3
  CLUS_2            1              8
  CLUS_3           21            173
D4V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            0              8
  CLUS_2            0              2
  CLUS_3           22            174

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           28             49
  CLUS_2           39             43
  CLUS_3           25             31
  CLUS_4            3              2
D5V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              4
  CLUS_2            2              0
  CLUS_3            0              1
D5V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           16             24
  CLUS_2           34             33
  CLUS_3            9             15
  CLUS_4           13             13
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, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              3
  CLUS_2            7              2
  CLUS_3           79            115
D5V8, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1              7
  CLUS_2            2              0
  CLUS_3           83            113

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           61             16
  CLUS_2           19             63
  CLUS_3           35             21
  CLUS_4            2              3
D6V4, multiclass
[1] "Remove cluster labels:" "TP53 WILD-TYPE"        
clus
  TP53 MUTATED TP53 WILD-TYPE 
             7              1 
  TCGA-A6-3810   TCGA-AG-A01W   TCGA-AG-A01Y   TCGA-AG-A020   TCGA-AG-A026 
"TP53 MUTATED" "TP53 MUTATED" "TP53 MUTATED" "TP53 MUTATED" "TP53 MUTATED" 
  TCGA-AG-A02N   TCGA-AG-A036 
"TP53 MUTATED" "TP53 MUTATED" 
D6V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           18             22
  CLUS_2           34             33
  CLUS_3           15              9
  CLUS_4           12             14
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, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              0
  CLUS_2            2              7
  CLUS_3          106             88
D6V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6              2
  CLUS_2            1              1
  CLUS_3          104             92

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             5              72
  CLUS_2            15              67
  CLUS_3             6              50
  CLUS_4             0               5
D7V4, multiclass
[1] "Remove cluster labels:" "SMAD4 MUTATED"         
clus
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1               7 
     TCGA-A6-2677      TCGA-A6-3810      TCGA-AG-A01W      TCGA-AG-A01Y 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02N      TCGA-AG-A036 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
D7V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             4              36
  CLUS_2            10              57
  CLUS_3             4              20
  CLUS_4             3              23
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, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               3
  CLUS_2             1               8
  CLUS_3            24             170
D7V8, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1               7
  CLUS_2             0               2
  CLUS_3            24             172

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               3                74
  CLUS_2              17                65
  CLUS_3               4                52
  CLUS_4               0                 5
D8V4, multiclass
[1] "Remove cluster labels:" "FAM123B MUTATED"       
clus
  FAM123B MUTATED FAM123B WILD-TYPE 
                1                 7 
       TCGA-A6-2677        TCGA-A6-3810        TCGA-AG-A01W        TCGA-AG-A01Y 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A026        TCGA-AG-A036 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
D8V5, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               2                38
  CLUS_2               7                60
  CLUS_3               2                22
  CLUS_4               5                21
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, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               0                 3
  CLUS_2               1                 8
  CLUS_3              23               171
D8V8, multiclass
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               0                 2
  CLUS_3              23               173

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              4               73
  CLUS_2             23               59
  CLUS_3              3               53
  CLUS_4              2                3
D9V4, multiclass
[1] "Remove cluster labels:" "PIK3CA MUTATED"        
clus
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               2                6 
      TCGA-A6-2677       TCGA-A6-3810       TCGA-AG-A01W       TCGA-AG-A01Y 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A026       TCGA-AG-A036 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
D9V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             11               29
  CLUS_2              9               58
  CLUS_3              1               23
  CLUS_4              6               20
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, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0                3
  CLUS_2              3                6
  CLUS_3             26              168
D9V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                7
  CLUS_2              0                2
  CLUS_3             28              168

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              73
  CLUS_2             9              73
  CLUS_3             2              54
  CLUS_4             0               5
D10V4, multiclass
[1] "Remove cluster labels:" "SMAD2 MUTATED"         
clus
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              1               7 
     TCGA-A6-2677      TCGA-A6-3810      TCGA-AG-A01Y      TCGA-AG-A020 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02N      TCGA-AG-A036 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
D10V5, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             2              38
  CLUS_2             3              64
  CLUS_3             2              22
  CLUS_4             3              23
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, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               3
  CLUS_2             0               9
  CLUS_3            14             180
D10V8, multiclass
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0               2
  CLUS_3            14             182

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               70
  CLUS_2              6               76
  CLUS_3              2               54
  CLUS_4              3                2
D11V4, multiclass
D11V5, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              3               37
  CLUS_2              5               62
  CLUS_3              1               23
  CLUS_4              3               23
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, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                3
  CLUS_2              0                9
  CLUS_3             15              179
D11V8, multiclass
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              0                2
  CLUS_3             15              181

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               76
  CLUS_2              8               74
  CLUS_3              0               56
  CLUS_4              0                5
D12V4, multiclass
D12V5, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0               40
  CLUS_2              4               63
  CLUS_3              0               24
  CLUS_4              3               23
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, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1                2
  CLUS_2              0                9
  CLUS_3              8              186
D12V8, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0                8
  CLUS_2              0                2
  CLUS_3              9              187

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             77
  CLUS_2            9             73
  CLUS_3            1             55
  CLUS_4            0              5
D13V4, multiclass
D13V5, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0             40
  CLUS_2            3             64
  CLUS_3            0             24
  CLUS_4            2             24
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, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0              3
  CLUS_2            0              9
  CLUS_3           10            184
D13V8, multiclass
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            0              2
  CLUS_3           10            186

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            1             76
  CLUS_2            2             80
  CLUS_3            3             53
  CLUS_4            0              5
D14V4, multiclass
D14V5, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             38
  CLUS_2            1             66
  CLUS_3            0             24
  CLUS_4            1             25
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, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0              3
  CLUS_2            0              9
  CLUS_3            6            188
D14V8, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            0              2
  CLUS_3            6            190

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             2              75
  CLUS_2             3              79
  CLUS_3             1              55
  CLUS_4             0               5
D15V4, multiclass
D15V5, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             2              38
  CLUS_2             0              67
  CLUS_3             0              24
  CLUS_4             1              25
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, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             0               3
  CLUS_2             0               9
  CLUS_3             6             188
D15V8, multiclass
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0               2
  CLUS_3             6             190

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                 1                  76
  CLUS_2                 2                  80
  CLUS_3                 2                  54
  CLUS_4                 1                   4
D16V4, multiclass
D16V5, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 3                  37
  CLUS_2                 1                  66
  CLUS_3                 0                  24
  CLUS_4                 1                  25
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, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 0                   3
  CLUS_2                 0                   9
  CLUS_3                 6                 188
D16V8, multiclass
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  CLUS_1                 0                   8
  CLUS_2                 0                   2
  CLUS_3                 6                 190

Clustering(17) Variable = KIAA1804 MUTATION ANALYSIS
D17V1, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                1                 56
  CLUS_3                6                 61
  CLUS_4                4                 35
D17V2, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                4                 36
  CLUS_2                2                 46
  CLUS_3                6                 55
  CLUS_4                2                 54
D17V3, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                4                 73
  CLUS_2                9                 73
  CLUS_3                1                 55
  CLUS_4                1                  4
D17V4, multiclass
[1] "Remove cluster labels:" "KIAA1804 MUTATED"      
clus
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 1                  7 
        TCGA-A6-2677         TCGA-A6-3810         TCGA-AG-A01W 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A026 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A036 
"KIAA1804 WILD-TYPE" 
D17V5, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                2                 38
  CLUS_2                6                 61
  CLUS_3                1                 23
  CLUS_4                4                 22
D17V6, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                 20
  CLUS_2               11                 98
  CLUS_3                2                 17
  CLUS_4                0                  9
D17V7, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  9
  CLUS_3               15                179
D17V8, multiclass
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                0                  2
  CLUS_3               15                181

Clustering(18) Variable = KRTAP5-5 MUTATION ANALYSIS
D18V1, 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
D18V2, 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
D18V3, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                2                 75
  CLUS_2                1                 81
  CLUS_3                1                 55
  CLUS_4                0                  5
D18V4, multiclass
D18V5, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                0                 40
  CLUS_2                3                 64
  CLUS_3                1                 23
  CLUS_4                0                 26
D18V6, 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
D18V7, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                0                  3
  CLUS_2                0                  9
  CLUS_3                3                191
D18V8, multiclass
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                0                  2
  CLUS_3                3                193

Clustering(19) Variable = PTEN MUTATION ANALYSIS
D19V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             40
  CLUS_2            0             57
  CLUS_3            1             66
  CLUS_4            4             35
D19V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             39
  CLUS_2            0             48
  CLUS_3            4             57
  CLUS_4            2             54
D19V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             77
  CLUS_2            6             76
  CLUS_3            1             55
  CLUS_4            0              5
D19V4, multiclass
D19V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2             38
  CLUS_2            1             66
  CLUS_3            0             24
  CLUS_4            1             25
D19V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             19
  CLUS_2            2            107
  CLUS_3            1             18
  CLUS_4            0              9
D19V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              3
  CLUS_2            1              8
  CLUS_3            6            188
D19V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1              7
  CLUS_2            0              2
  CLUS_3            6            190

Clustering(20) Variable = ACOT4 MUTATION ANALYSIS
D20V1, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             0              57
  CLUS_3             1              66
  CLUS_4             0              39
D20V2, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             0              40
  CLUS_2             1              47
  CLUS_3             2              59
  CLUS_4             0              56
D20V3, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             0              77
  CLUS_2             2              80
  CLUS_3             1              55
  CLUS_4             0               5
D20V4, multiclass
D20V5, 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" 
D20V6, 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" 
D20V7, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             0               3
  CLUS_2             0               9
  CLUS_3             3             191
D20V8, multiclass
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0               2
  CLUS_3             3             193

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              75
  CLUS_2            11              71
  CLUS_3             0              56
  CLUS_4             0               5
D21V4, multiclass
[1] "Remove cluster labels:" "MYO1B MUTATED"         
clus
  MYO1B MUTATED MYO1B WILD-TYPE 
              1               7 
     TCGA-A6-2677      TCGA-A6-3810      TCGA-AG-A01W      TCGA-AG-A01Y 
"MYO1B WILD-TYPE" "MYO1B WILD-TYPE" "MYO1B WILD-TYPE" "MYO1B WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A026      TCGA-AG-A036 
"MYO1B WILD-TYPE" "MYO1B WILD-TYPE" "MYO1B WILD-TYPE" 
D21V5, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             3              37
  CLUS_2             0              67
  CLUS_3             1              23
  CLUS_4             3              23
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, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             0               3
  CLUS_2             0               9
  CLUS_3            12             182
D21V8, multiclass
        clus
vv       MYO1B MUTATED MYO1B WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0               2
  CLUS_3            12             184

Clustering(22) Variable = PCBP1 MUTATION ANALYSIS
D22V1, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              42
  CLUS_2             1              56
  CLUS_3             2              65
  CLUS_4             3              36
D22V2, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             2              38
  CLUS_2             1              47
  CLUS_3             2              59
  CLUS_4             1              55
D22V3, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             1              76
  CLUS_2             3              79
  CLUS_3             2              54
  CLUS_4             0               5
D22V4, multiclass
D22V5, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              40
  CLUS_2             2              65
  CLUS_3             0              24
  CLUS_4             1              25
D22V6, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             2             107
  CLUS_3             1              18
  CLUS_4             0               9
D22V7, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0               3
  CLUS_2             0               9
  CLUS_3             5             189
D22V8, multiclass
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             0               2
  CLUS_3             5             191

Clustering(23) Variable = GGT1 MUTATION ANALYSIS
D23V1, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            203 
    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-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3890 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A032     TCGA-AY-4070     TCGA-AY-4071 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D23V2, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            203 
    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-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3575 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3890 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02X 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A032     TCGA-AY-4070     TCGA-AY-4071 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D23V3, multiclass
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  CLUS_1            0             77
  CLUS_2            3             79
  CLUS_3            0             56
  CLUS_4            0              5
D23V4, multiclass
D23V5, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            155 
    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     TCGA-AF-2689     TCGA-AF-3400 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3578     TCGA-AG-3580 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3609     TCGA-AG-3612 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01W 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026     TCGA-AG-A02G 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D23V6, multiclass
[1] "Remove cluster labels:" "GGT1 MUTATED"          
clus
  GGT1 MUTATED GGT1 WILD-TYPE 
             2            155 
    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     TCGA-AF-2689     TCGA-AF-3400 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3574     TCGA-AG-3578     TCGA-AG-3580 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3609     TCGA-AG-3612 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3878     TCGA-AG-3881     TCGA-AG-3882 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01W 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A026     TCGA-AG-A02G 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A036 
"GGT1 WILD-TYPE" "GGT1 WILD-TYPE" "GGT1 WILD-TYPE" 
D23V7, multiclass
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  CLUS_1            0              3
  CLUS_2            0              9
  CLUS_3            3            191
D23V8, multiclass
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            0              2
  CLUS_3            3            193

Clustering(24) Variable = ACVR1B MUTATION ANALYSIS
D24V1, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              3               39
  CLUS_2              2               55
  CLUS_3              2               65
  CLUS_4              4               35
D24V2, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              0               40
  CLUS_2              3               45
  CLUS_3              5               56
  CLUS_4              3               53
D24V3, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              2               75
  CLUS_2             10               72
  CLUS_3              2               54
  CLUS_4              0                5
D24V4, multiclass
D24V5, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              2               38
  CLUS_2              5               62
  CLUS_3              1               23
  CLUS_4              3               23
D24V6, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              1               19
  CLUS_2              7              102
  CLUS_3              3               16
  CLUS_4              0                9
D24V7, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              0                3
  CLUS_2              1                8
  CLUS_3             13              181
D24V8, multiclass
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  CLUS_1              0                8
  CLUS_2              0                2
  CLUS_3             14              182
                    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")
