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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/376786/CESC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/CESC-TP/2907374/1.GDAC_mergedClustering.Finished/CESC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC-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=CESC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=134, in cluster file=39, common to both=39
[1] "Reduce the number of clustering variables from 13 to 9."
[1]  9 39
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               30 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               9               30 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              4              35 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              4              35 
[1] "PRG4 MUTATION ANALYSIS"
[1] 3
  PRG4 MUTATED PRG4 WILD-TYPE 
             5             34 
  PRG4 MUTATED PRG4 WILD-TYPE 
             5             34 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              34 
  CDC27 MUTATED CDC27 WILD-TYPE 
              5              34 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               6               33 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               6               33 
[1] "MAPK1 MUTATION ANALYSIS"
[1] 3
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              3              36 
  MAPK1 MUTATED MAPK1 WILD-TYPE 
              3              36 
[1] "SSX7 MUTATION ANALYSIS"
[1] 3
  SSX7 MUTATED SSX7 WILD-TYPE 
             3             36 
  SSX7 MUTATED SSX7 WILD-TYPE 
             3             36 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               36 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               36 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             4             35 
  PRB2 MUTATED PRB2 WILD-TYPE 
             4             35 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 39 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 39 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PIK3CA MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               12
  CLUS_2              0                7
  CLUS_3              6                8
D1V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               14
  CLUS_2              6               11
  CLUS_3              1                5
D1V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               14
  CLUS_2              1                8
  CLUS_3              1                7
D1V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                3
  CLUS_2              7               18
  CLUS_3              1                8
D1V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               14
  CLUS_2              2                6
  CLUS_3              3               10
D1V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2                7
  CLUS_2              7               14
  CLUS_3              0                9

Clustering(2) Variable = TMCC1 MUTATION ANALYSIS
D2V1, multiclass
[1] "Remove cluster labels:" "TMCC1 MUTATED"         
clus
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              2              34 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-BI-A20A      TCGA-C5-A0TN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1BE      TCGA-C5-A1BF      TCGA-C5-A1BI      TCGA-C5-A1BJ 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1BL      TCGA-C5-A1BM      TCGA-C5-A1BN      TCGA-C5-A1M5 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1M6      TCGA-C5-A1M8      TCGA-C5-A1M9      TCGA-C5-A1ME 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MF      TCGA-C5-A1MH      TCGA-C5-A1MI      TCGA-C5-A1MJ 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1ML      TCGA-C5-A1MN      TCGA-C5-A1MP 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK      TCGA-DS-A0VL 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-EA-A1QT      TCGA-EX-A1H5 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
D2V2, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2              14
  CLUS_2             2              15
  CLUS_3             0               6
D2V3, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             2               7
  CLUS_3             0               8
D2V4, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             2              23
  CLUS_3             0               9
D2V5, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             3              15
  CLUS_2             1               7
  CLUS_3             0              13
D2V6, multiclass
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              18
  CLUS_3             1               8

Clustering(3) Variable = PRG4 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  CLUS_1            0             15
  CLUS_2            1              6
  CLUS_3            2             12
D3V2, multiclass
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            3             14
  CLUS_3            0              6
D3V3, multiclass
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            4              5
  CLUS_3            0              8
D3V4, multiclass
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  CLUS_1            2              2
  CLUS_2            2             23
  CLUS_3            1              8
D3V5, multiclass
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  CLUS_1            3             15
  CLUS_2            2              6
  CLUS_3            0             13
D3V6, multiclass
        clus
vv       PRG4 MUTATED PRG4 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            3             18
  CLUS_3            2              7

Clustering(4) Variable = CDC27 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             1               6
  CLUS_3             0              14
D4V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             4              12
  CLUS_2             1              16
  CLUS_3             0               6
D4V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              19
  CLUS_2             3               6
  CLUS_3             0               8
D4V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2               2
  CLUS_2             3              22
  CLUS_3             0               9
D4V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3              15
  CLUS_2             1               7
  CLUS_3             1              12
D4V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              19
  CLUS_3             3               6

Clustering(5) Variable = NFE2L2 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              2                5
  CLUS_3              2               12
D5V2, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               12
  CLUS_2              2               15
  CLUS_3              0                6
D5V3, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               17
  CLUS_2              2                7
  CLUS_3              0                8
D5V4, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                4
  CLUS_2              6               19
  CLUS_3              0                9
D5V5, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              4               14
  CLUS_2              2                6
  CLUS_3              0               13
D5V6, multiclass
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3               18
  CLUS_3              3                6

Clustering(6) Variable = MAPK1 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             0               7
  CLUS_3             3              11
D6V2, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             1              15
  CLUS_2             2              15
  CLUS_3             0               6
D6V3, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             3              18
  CLUS_2             0               9
  CLUS_3             0               8
D6V4, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             3              22
  CLUS_3             0               9
D6V5, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             3              15
  CLUS_2             0               8
  CLUS_3             0              13
D6V6, multiclass
        clus
vv       MAPK1 MUTATED MAPK1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              19
  CLUS_3             1               8

Clustering(7) Variable = SSX7 MUTATION ANALYSIS
D7V1, multiclass
[1] "Remove cluster labels:" "SSX7 MUTATED"          
clus
  SSX7 MUTATED SSX7 WILD-TYPE 
             1             35 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ     TCGA-C5-A1BK 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-C5-A1BL     TCGA-C5-A1BM     TCGA-C5-A1BN     TCGA-C5-A1M5 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8     TCGA-C5-A1M9 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH     TCGA-C5-A1MI 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-C5-A1MJ     TCGA-C5-A1MK     TCGA-C5-A1ML     TCGA-C5-A1MN 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-C5-A1MP     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-EA-A1QT 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
    TCGA-EX-A1H5     TCGA-FU-A23K     TCGA-FU-A23L 
"SSX7 WILD-TYPE" "SSX7 WILD-TYPE" "SSX7 WILD-TYPE" 
D7V2, multiclass
        clus
vv       SSX7 MUTATED SSX7 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            1             16
  CLUS_3            0              6
D7V3, multiclass
        clus
vv       SSX7 MUTATED SSX7 WILD-TYPE
  CLUS_1            1             20
  CLUS_2            2              7
  CLUS_3            0              8
D7V4, multiclass
        clus
vv       SSX7 MUTATED SSX7 WILD-TYPE
  CLUS_1            2              2
  CLUS_2            1             24
  CLUS_3            0              9
D7V5, multiclass
        clus
vv       SSX7 MUTATED SSX7 WILD-TYPE
  CLUS_1            2             16
  CLUS_2            1              7
  CLUS_3            0             13
D7V6, multiclass
        clus
vv       SSX7 MUTATED SSX7 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             19
  CLUS_3            1              8

Clustering(8) Variable = UGT3A2 MUTATION ANALYSIS
D8V1, multiclass
[1] "Remove cluster labels:" "UGT3A2 MUTATED"        
clus
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               1               35 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-BI-A20A       TCGA-C5-A0TN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BE       TCGA-C5-A1BF       TCGA-C5-A1BI       TCGA-C5-A1BJ 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BK       TCGA-C5-A1BL       TCGA-C5-A1BM       TCGA-C5-A1BN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1M6       TCGA-C5-A1M7       TCGA-C5-A1M8 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M9       TCGA-C5-A1ME       TCGA-C5-A1MF       TCGA-C5-A1MH 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MI       TCGA-C5-A1MJ       TCGA-C5-A1MK       TCGA-C5-A1ML 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-C5-A1MP       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VN       TCGA-EA-A1QT 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-EX-A1H5       TCGA-FU-A23K       TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
D8V2, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              2               14
  CLUS_2              1               16
  CLUS_3              0                6
D8V3, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              0               21
  CLUS_2              3                6
  CLUS_3              0                8
D8V4, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              2                2
  CLUS_2              1               24
  CLUS_3              0                9
D8V5, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              2               16
  CLUS_2              1                7
  CLUS_3              0               13
D8V6, multiclass
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1               20
  CLUS_3              2                7

Clustering(9) Variable = PRB2 MUTATION ANALYSIS
D9V1, multiclass
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2             34 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-BI-A20A     TCGA-C5-A0TN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1BE     TCGA-C5-A1BF     TCGA-C5-A1BI     TCGA-C5-A1BJ 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1BK     TCGA-C5-A1BL     TCGA-C5-A1BM     TCGA-C5-A1BN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1M6     TCGA-C5-A1M7     TCGA-C5-A1M8 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1M9     TCGA-C5-A1ME     TCGA-C5-A1MF     TCGA-C5-A1MH 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1MI     TCGA-C5-A1MJ     TCGA-C5-A1MK     TCGA-C5-A1ML 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-EA-A1QT     TCGA-EX-A1H5 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FU-A23K     TCGA-FU-A23L 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
D9V2, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2             14
  CLUS_2            2             15
  CLUS_3            0              6
D9V3, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2             19
  CLUS_2            2              7
  CLUS_3            0              8
D9V4, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2              2
  CLUS_2            2             23
  CLUS_3            0              9
D9V5, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2             16
  CLUS_2            2              6
  CLUS_3            0             13
D9V6, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             19
  CLUS_3            2              7
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
