
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/350178/LAML-TB.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LAML-TB/2666799/1.GDAC_mergedClustering.Finished/LAML-TB.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LAML-TB", "-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=LAML-TB"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=200, in cluster file=197, common to both=197
[1] "Reduce the number of clustering variables from 28 to 24."
[1]  24 197
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            182 
  NRAS MUTATED NRAS WILD-TYPE 
            15            182 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           12           185 
  WT1 MUTATED WT1 WILD-TYPE 
           12           185 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             18             179 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             18             179 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              51              146 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              51              146 
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            56            141 
  FLT3 MUTATED FLT3 WILD-TYPE 
            56            141 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            19            178 
  IDH1 MUTATED IDH1 WILD-TYPE 
            19            178 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            177 
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            177 
[1] "NPM1 MUTATION ANALYSIS"
[1] 3
  NPM1 MUTATED NPM1 WILD-TYPE 
            54            143 
  NPM1 MUTATED NPM1 WILD-TYPE 
            54            143 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             189 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             189 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            15            182 
  TP53 MUTATED TP53 WILD-TYPE 
            15            182 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             8            189 
  KRAS MUTATED KRAS WILD-TYPE 
             8            189 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              188 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              188 
[1] "TET2 MUTATION ANALYSIS"
[1] 3
  TET2 MUTATED TET2 WILD-TYPE 
            17            180 
  TET2 MUTATED TET2 WILD-TYPE 
            17            180 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
            8           189 
  KIT MUTATED KIT WILD-TYPE 
            8           189 
[1] "PHF6 MUTATION ANALYSIS"
[1] 3
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            191 
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            191 
[1] "SMC1A MUTATION ANALYSIS"
[1] 3
  SMC1A MUTATED SMC1A WILD-TYPE 
              7             190 
  SMC1A MUTATED SMC1A WILD-TYPE 
              7             190 
[1] "SMC3 MUTATION ANALYSIS"
[1] 3
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            190 
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            190 
[1] "RAD21 MUTATION ANALYSIS"
[1] 3
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             192 
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             192 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             191 
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             191 
[1] "FAM5C MUTATION ANALYSIS"
[1] 3
  FAM5C MUTATED FAM5C WILD-TYPE 
              5             192 
  FAM5C MUTATED FAM5C WILD-TYPE 
              5             192 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            194 
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            194 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             192 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             192 
[1] "PHACTR1 MUTATION ANALYSIS"
[1] 3
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               194 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               194 
[1] "DIS3 MUTATION ANALYSIS"
[1] 3
  DIS3 MUTATED DIS3 WILD-TYPE 
             3            194 
  DIS3 MUTATED DIS3 WILD-TYPE 
             3            194 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 197 columns.

Variable 1:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	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 197 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NRAS MUTATION ANALYSIS
D1V1, multiclass
D1V2, multiclass
D1V3, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             68
  CLUS_2            5             47
  CLUS_3            2             43
D1V4, binary
                cls
clus               0   1
  NRAS MUTATED     5   7
  NRAS WILD-TYPE  52 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5    7
  NRAS WILD-TYPE   52  106
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            5             52
  CLUS_2            7            106
D1V5, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            7             77
  CLUS_2            3             37
  CLUS_3            4             56
D1V6, multiclass
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  CLUS_1            3             35
  CLUS_2            7             74
  CLUS_3            4             61

Clustering(2) Variable = WT1 MUTATION ANALYSIS
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           2            71
  CLUS_2           2            50
  CLUS_3           6            39
D2V4, binary
               cls
clus              0   1
  WT1 MUTATED     3   7
  WT1 WILD-TYPE  54 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      3    7
  WT1 WILD-TYPE   54  106
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           3            54
  CLUS_2           7           106
D2V5, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           6            78
  CLUS_2           1            39
  CLUS_3           4            56
D2V6, multiclass
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  CLUS_1           1            37
  CLUS_2           7            74
  CLUS_3           3            62

Clustering(3) Variable = RUNX1 MUTATION ANALYSIS
D3V1, multiclass
D3V2, multiclass
D3V3, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1            13              60
  CLUS_2             3              49
  CLUS_3             0              45
D3V4, binary
                 cls
clus               0  1
  RUNX1 MUTATED    2 14
  RUNX1 WILD-TYPE 55 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      2   14
  RUNX1 WILD-TYPE   55   99
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             2              55
  CLUS_2            14              99
D3V5, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             2              82
  CLUS_2             4              36
  CLUS_3            10              50
D3V6, multiclass
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  CLUS_1             4              34
  CLUS_2             0              81
  CLUS_3            12              53

Clustering(4) Variable = DNMT3A MUTATION ANALYSIS
D4V1, multiclass
D4V2, multiclass
D4V3, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             11               62
  CLUS_2             20               32
  CLUS_3             12               33
D4V4, binary
                  cls
clus                0  1
  DNMT3A MUTATED   18 25
  DNMT3A WILD-TYPE 39 88
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     18   25
  DNMT3A WILD-TYPE   39   88
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             18               39
  CLUS_2             25               88
D4V5, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1             33               51
  CLUS_2              3               37
  CLUS_3              9               51
D4V6, multiclass
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  CLUS_1              3               35
  CLUS_2             34               47
  CLUS_3              8               57

Clustering(5) Variable = FLT3 MUTATION ANALYSIS
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            6             67
  CLUS_2           20             32
  CLUS_3           23             22
D5V4, binary
                cls
clus              0  1
  FLT3 MUTATED   23 26
  FLT3 WILD-TYPE 34 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     23   26
  FLT3 WILD-TYPE   34   87
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           23             34
  CLUS_2           26             87
D5V5, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1           36             48
  CLUS_2            4             36
  CLUS_3           14             46
D5V6, multiclass
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  CLUS_1            4             34
  CLUS_2           38             43
  CLUS_3           12             53

Clustering(6) Variable = IDH1 MUTATION ANALYSIS
D6V1, multiclass
D6V2, multiclass
D6V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            7             66
  CLUS_2            3             49
  CLUS_3            6             39
D6V4, binary
                cls
clus               0   1
  IDH1 MUTATED     3  13
  IDH1 WILD-TYPE  54 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3   13
  IDH1 WILD-TYPE   54  100
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             54
  CLUS_2           13            100
D6V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           12             72
  CLUS_2            3             37
  CLUS_3            4             56
D6V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             35
  CLUS_2           12             69
  CLUS_3            4             61

Clustering(7) Variable = IDH2 MUTATION ANALYSIS
D7V1, multiclass
D7V2, multiclass
D7V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            8             65
  CLUS_2            6             46
  CLUS_3            3             42
D7V4, binary
                cls
clus               0   1
  IDH2 MUTATED     6  11
  IDH2 WILD-TYPE  51 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      6   11
  IDH2 WILD-TYPE   51  102
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            6             51
  CLUS_2           11            102
D7V5, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            7             77
  CLUS_2            4             36
  CLUS_3            6             54
D7V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3             35
  CLUS_2            7             74
  CLUS_3            7             58

Clustering(8) Variable = NPM1 MUTATION ANALYSIS
D8V1, multiclass
D8V2, multiclass
D8V3, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            1             72
  CLUS_2           22             30
  CLUS_3           25             20
D8V4, binary
                cls
clus              0  1
  NPM1 MUTATED   24 24
  NPM1 WILD-TYPE 33 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPM1 MUTATED     24   24
  NPM1 WILD-TYPE   33   89
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           24             33
  CLUS_2           24             89
D8V5, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1           50             34
  CLUS_2            0             40
  CLUS_3            1             59
D8V6, multiclass
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  CLUS_1            0             38
  CLUS_2           50             31
  CLUS_3            1             64

Clustering(9) Variable = U2AF1 MUTATION ANALYSIS
D9V1, multiclass
D9V2, multiclass
D9V3, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             5              68
  CLUS_2             2              50
  CLUS_3             0              45
D9V4, binary
                 cls
clus                0   1
  U2AF1 MUTATED     1   6
  U2AF1 WILD-TYPE  56 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      1    6
  U2AF1 WILD-TYPE   56  107
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              56
  CLUS_2             6             107
D9V5, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             1              83
  CLUS_2             3              37
  CLUS_3             3              57
D9V6, multiclass
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  CLUS_1             3              35
  CLUS_2             1              80
  CLUS_3             3              62

Clustering(10) Variable = TP53 MUTATION ANALYSIS
D10V1, multiclass
D10V2, multiclass
D10V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             61
  CLUS_2            1             51
  CLUS_3            0             45
D10V4, binary
                cls
clus               0   1
  TP53 MUTATED     1  12
  TP53 WILD-TYPE  56 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   12
  TP53 WILD-TYPE   56  101
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             56
  CLUS_2           12            101
D10V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             82
  CLUS_2            9             31
  CLUS_3            3             57
D10V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             29
  CLUS_2            1             80
  CLUS_3            4             61

Clustering(11) Variable = KRAS MUTATION ANALYSIS
D11V1, multiclass
D11V2, multiclass
D11V3, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             69
  CLUS_2            3             49
  CLUS_3            0             45
D11V4, binary
                cls
clus               0   1
  KRAS MUTATED     4   3
  KRAS WILD-TYPE  53 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    3
  KRAS WILD-TYPE   53  110
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             53
  CLUS_2            3            110
D11V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             80
  CLUS_2            3             37
  CLUS_3            0             60
D11V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            3             35
  CLUS_2            4             77
  CLUS_3            0             65

Clustering(12) Variable = PTPN11 MUTATION ANALYSIS
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              1               72
  CLUS_2              2               50
  CLUS_3              5               40
D12V4, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     3   5
  PTPN11 WILD-TYPE  54 108
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      3    5
  PTPN11 WILD-TYPE   54  108
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              3               54
  CLUS_2              5              108
D12V5, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              7               77
  CLUS_2              1               39
  CLUS_3              1               59
D12V6, multiclass
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  CLUS_1              1               37
  CLUS_2              6               75
  CLUS_3              2               63

Clustering(13) Variable = TET2 MUTATION ANALYSIS
D13V1, multiclass
D13V2, multiclass
D13V3, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            9             64
  CLUS_2            2             50
  CLUS_3            4             41
D13V4, binary
                cls
clus               0   1
  TET2 MUTATED     4  11
  TET2 WILD-TYPE  53 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET2 MUTATED      4   11
  TET2 WILD-TYPE   53  102
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            4             53
  CLUS_2           11            102
D13V5, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            8             76
  CLUS_2            2             38
  CLUS_3            7             53
D13V6, multiclass
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  CLUS_1            3             35
  CLUS_2           10             71
  CLUS_3            4             61

Clustering(14) Variable = KIT MUTATION ANALYSIS
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           4            69
  CLUS_2           3            49
  CLUS_3           0            45
D14V4, binary
               cls
clus              0   1
  KIT MUTATED     3   4
  KIT WILD-TYPE  54 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      3    4
  KIT WILD-TYPE   54  109
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           3            54
  CLUS_2           4           109
D14V5, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           1            83
  CLUS_2           3            37
  CLUS_3           4            56
D14V6, multiclass
        clus
vv       KIT MUTATED KIT WILD-TYPE
  CLUS_1           3            35
  CLUS_2           1            80
  CLUS_3           4            61

Clustering(15) Variable = PHF6 MUTATION ANALYSIS
D15V1, multiclass
D15V2, multiclass
D15V3, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            2             71
  CLUS_2            1             51
  CLUS_3            2             43
D15V4, binary
                cls
clus               0   1
  PHF6 MUTATED     0   5
  PHF6 WILD-TYPE  57 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF6 MUTATED      0    5
  PHF6 WILD-TYPE   57  108
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            0             57
  CLUS_2            5            108
D15V5, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            2             82
  CLUS_2            0             40
  CLUS_3            3             57
D15V6, multiclass
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  CLUS_1            0             38
  CLUS_2            1             80
  CLUS_3            4             61

Clustering(16) Variable = SMC1A MUTATION ANALYSIS
D16V1, multiclass
D16V2, multiclass
D16V3, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             2              71
  CLUS_2             4              48
  CLUS_3             1              44
D16V4, binary
                 cls
clus                0   1
  SMC1A MUTATED     5   2
  SMC1A WILD-TYPE  52 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1A MUTATED      5    2
  SMC1A WILD-TYPE   52  111
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             5              52
  CLUS_2             2             111
D16V5, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             6              78
  CLUS_2             0              40
  CLUS_3             1              59
D16V6, multiclass
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  CLUS_1             0              38
  CLUS_2             6              75
  CLUS_3             1              64

Clustering(17) Variable = SMC3 MUTATION ANALYSIS
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            2             71
  CLUS_2            2             50
  CLUS_3            3             42
D17V4, binary
                cls
clus               0   1
  SMC3 MUTATED     1   6
  SMC3 WILD-TYPE  56 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      1    6
  SMC3 WILD-TYPE   56  107
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            1             56
  CLUS_2            6            107
D17V5, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            4             80
  CLUS_2            0             40
  CLUS_3            3             57
D17V6, multiclass
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  CLUS_1            0             38
  CLUS_2            4             77
  CLUS_3            3             62

Clustering(18) Variable = RAD21 MUTATION ANALYSIS
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             1              72
  CLUS_2             2              50
  CLUS_3             2              43
D18V4, binary
                 cls
clus                0   1
  RAD21 MUTATED     2   3
  RAD21 WILD-TYPE  55 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED      2    3
  RAD21 WILD-TYPE   55  110
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             2              55
  CLUS_2             3             110
D18V5, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             4              80
  CLUS_2             0              40
  CLUS_3             1              59
D18V6, multiclass
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  CLUS_1             0              38
  CLUS_2             4              77
  CLUS_3             1              64

Clustering(19) Variable = STAG2 MUTATION ANALYSIS
D19V1, multiclass
D19V2, multiclass
D19V3, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              71
  CLUS_2             0              52
  CLUS_3             3              42
D19V4, binary
                 cls
clus                0   1
  STAG2 MUTATED     0   5
  STAG2 WILD-TYPE  57 108
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    5
  STAG2 WILD-TYPE   57  108
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             0              57
  CLUS_2             5             108
D19V5, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             3              81
  CLUS_2             1              39
  CLUS_3             1              59
D19V6, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             1              37
  CLUS_2             4              77
  CLUS_3             0              65

Clustering(20) Variable = FAM5C MUTATION ANALYSIS
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       FAM5C MUTATED FAM5C WILD-TYPE
  CLUS_1             2              71
  CLUS_2             1              51
  CLUS_3             2              43
D20V4, binary
                 cls
clus                0   1
  FAM5C MUTATED     1   4
  FAM5C WILD-TYPE  56 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM5C MUTATED      1    4
  FAM5C WILD-TYPE   56  109
        clus
vv       FAM5C MUTATED FAM5C WILD-TYPE
  CLUS_1             1              56
  CLUS_2             4             109
D20V5, multiclass
        clus
vv       FAM5C MUTATED FAM5C WILD-TYPE
  CLUS_1             2              82
  CLUS_2             1              39
  CLUS_3             2              58
D20V6, multiclass
        clus
vv       FAM5C MUTATED FAM5C WILD-TYPE
  CLUS_1             1              37
  CLUS_2             2              79
  CLUS_3             2              63

Clustering(21) Variable = EZH2 MUTATION ANALYSIS
D21V1, multiclass
D21V2, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             2            189 
    TCGA-AB-2802     TCGA-AB-2803     TCGA-AB-2804     TCGA-AB-2805 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2806     TCGA-AB-2807     TCGA-AB-2808     TCGA-AB-2809 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2810     TCGA-AB-2811     TCGA-AB-2812     TCGA-AB-2813 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2814     TCGA-AB-2816     TCGA-AB-2818     TCGA-AB-2819 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2820     TCGA-AB-2821     TCGA-AB-2822     TCGA-AB-2823 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2824     TCGA-AB-2825     TCGA-AB-2826     TCGA-AB-2827 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2828     TCGA-AB-2829     TCGA-AB-2830     TCGA-AB-2831 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2832     TCGA-AB-2833     TCGA-AB-2834     TCGA-AB-2835 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2836     TCGA-AB-2837     TCGA-AB-2838     TCGA-AB-2839 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2840     TCGA-AB-2841     TCGA-AB-2842     TCGA-AB-2843 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2844     TCGA-AB-2845     TCGA-AB-2846     TCGA-AB-2847 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2848     TCGA-AB-2849     TCGA-AB-2851     TCGA-AB-2853 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2854     TCGA-AB-2855     TCGA-AB-2857     TCGA-AB-2858 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2860     TCGA-AB-2861     TCGA-AB-2862     TCGA-AB-2863 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2866     TCGA-AB-2867     TCGA-AB-2868     TCGA-AB-2869 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2870     TCGA-AB-2871     TCGA-AB-2872     TCGA-AB-2873 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2874     TCGA-AB-2875     TCGA-AB-2876     TCGA-AB-2877 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2878     TCGA-AB-2879     TCGA-AB-2880     TCGA-AB-2881 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2882     TCGA-AB-2883     TCGA-AB-2884     TCGA-AB-2885 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2886     TCGA-AB-2888     TCGA-AB-2889     TCGA-AB-2890 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2891     TCGA-AB-2892     TCGA-AB-2893     TCGA-AB-2894 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2895     TCGA-AB-2896     TCGA-AB-2897     TCGA-AB-2898 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2899     TCGA-AB-2900     TCGA-AB-2901     TCGA-AB-2903 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2904     TCGA-AB-2906     TCGA-AB-2907     TCGA-AB-2908 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2909     TCGA-AB-2910     TCGA-AB-2911     TCGA-AB-2912 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2913     TCGA-AB-2914     TCGA-AB-2915     TCGA-AB-2916 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2917     TCGA-AB-2918     TCGA-AB-2919     TCGA-AB-2920 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2921     TCGA-AB-2922     TCGA-AB-2923     TCGA-AB-2924 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2925     TCGA-AB-2926     TCGA-AB-2927     TCGA-AB-2928 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2929     TCGA-AB-2930     TCGA-AB-2931     TCGA-AB-2932 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2933     TCGA-AB-2934     TCGA-AB-2935     TCGA-AB-2936 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2937     TCGA-AB-2938     TCGA-AB-2939     TCGA-AB-2940 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2941     TCGA-AB-2942     TCGA-AB-2943     TCGA-AB-2945 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2946     TCGA-AB-2947     TCGA-AB-2948     TCGA-AB-2949 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2950     TCGA-AB-2952     TCGA-AB-2954     TCGA-AB-2955 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2956     TCGA-AB-2957     TCGA-AB-2959     TCGA-AB-2963 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2964     TCGA-AB-2965     TCGA-AB-2966     TCGA-AB-2967 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2968     TCGA-AB-2969     TCGA-AB-2970     TCGA-AB-2971 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2972     TCGA-AB-2973     TCGA-AB-2974     TCGA-AB-2975 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2976     TCGA-AB-2977     TCGA-AB-2978     TCGA-AB-2979 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2980     TCGA-AB-2981     TCGA-AB-2982     TCGA-AB-2983 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2984     TCGA-AB-2985     TCGA-AB-2986     TCGA-AB-2987 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2988     TCGA-AB-2989     TCGA-AB-2990     TCGA-AB-2991 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2992     TCGA-AB-2993     TCGA-AB-2995     TCGA-AB-2996 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-2997     TCGA-AB-2998     TCGA-AB-2999     TCGA-AB-3000 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-3001     TCGA-AB-3002     TCGA-AB-3005     TCGA-AB-3006 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-3007     TCGA-AB-3008     TCGA-AB-3009     TCGA-AB-3011 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-AB-3012 
"EZH2 WILD-TYPE" 
D21V3, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            3             70
  CLUS_2            0             52
  CLUS_3            0             45
D21V4, binary
                cls
clus               0   1
  EZH2 MUTATED     1   2
  EZH2 WILD-TYPE  56 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      1    2
  EZH2 WILD-TYPE   56  111
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            1             56
  CLUS_2            2            111
D21V5, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            0             84
  CLUS_2            1             39
  CLUS_3            2             58
D21V6, multiclass
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  CLUS_1            1             37
  CLUS_2            0             81
  CLUS_3            2             63

Clustering(22) Variable = ASXL1 MUTATION ANALYSIS
D22V1, multiclass
D22V2, multiclass
D22V3, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             3              70
  CLUS_2             0              52
  CLUS_3             0              45
D22V4, binary
                 cls
clus                0   1
  ASXL1 MUTATED     0   3
  ASXL1 WILD-TYPE  57 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      0    3
  ASXL1 WILD-TYPE   57  110
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             0              57
  CLUS_2             3             110
D22V5, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             0              84
  CLUS_2             1              39
  CLUS_3             2              58
D22V6, multiclass
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  CLUS_1             1              37
  CLUS_2             0              81
  CLUS_3             2              63

Clustering(23) Variable = PHACTR1 MUTATION ANALYSIS
D23V1, multiclass
[1] "Remove cluster labels:" "PHACTR1 MUTATED"       
clus
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                2               186 
       TCGA-AB-2803        TCGA-AB-2804        TCGA-AB-2805        TCGA-AB-2806 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2807        TCGA-AB-2808        TCGA-AB-2809        TCGA-AB-2810 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2811        TCGA-AB-2812        TCGA-AB-2813        TCGA-AB-2814 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2816        TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2820        TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2824        TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2827 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2828        TCGA-AB-2829        TCGA-AB-2830        TCGA-AB-2831 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2850 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2851        TCGA-AB-2853        TCGA-AB-2854        TCGA-AB-2855 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2857        TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2861        TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2864 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867        TCGA-AB-2869 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2870        TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2874        TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2878 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881        TCGA-AB-2882 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2883        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2892        TCGA-AB-2893        TCGA-AB-2894        TCGA-AB-2895 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898        TCGA-AB-2899 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903        TCGA-AB-2904 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2905        TCGA-AB-2906        TCGA-AB-2907        TCGA-AB-2908 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2909        TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2913        TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2917 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2922 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2923        TCGA-AB-2924        TCGA-AB-2925        TCGA-AB-2926 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2945        TCGA-AB-2946        TCGA-AB-2947 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2948        TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2954        TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2957 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2959        TCGA-AB-2963        TCGA-AB-2964        TCGA-AB-2965 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2966        TCGA-AB-2967        TCGA-AB-2968        TCGA-AB-2969 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972        TCGA-AB-2973 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2974        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2989        TCGA-AB-2990        TCGA-AB-2991 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2992        TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2996        TCGA-AB-2997        TCGA-AB-2998        TCGA-AB-2999 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3000        TCGA-AB-3001        TCGA-AB-3002        TCGA-AB-3005 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3006        TCGA-AB-3007        TCGA-AB-3008        TCGA-AB-3009 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3011        TCGA-AB-3012 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
D23V2, multiclass
D23V3, multiclass
[1] "Remove cluster labels:" "PHACTR1 MUTATED"       
clus
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                2               168 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2816        TCGA-AB-2817 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820        TCGA-AB-2821 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2833        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2843        TCGA-AB-2844 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2845        TCGA-AB-2846        TCGA-AB-2847        TCGA-AB-2848 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2849        TCGA-AB-2851        TCGA-AB-2853        TCGA-AB-2854 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2855        TCGA-AB-2857        TCGA-AB-2858        TCGA-AB-2859 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862        TCGA-AB-2863 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867        TCGA-AB-2869 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2870        TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2874        TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2880        TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2885        TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2889        TCGA-AB-2890        TCGA-AB-2891        TCGA-AB-2895 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898        TCGA-AB-2899 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903        TCGA-AB-2904 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910        TCGA-AB-2911 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914        TCGA-AB-2915 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2917        TCGA-AB-2918        TCGA-AB-2919        TCGA-AB-2920 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925        TCGA-AB-2927 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930        TCGA-AB-2931 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934        TCGA-AB-2935 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938        TCGA-AB-2939 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942        TCGA-AB-2943 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2946        TCGA-AB-2948        TCGA-AB-2949        TCGA-AB-2950 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2952        TCGA-AB-2954        TCGA-AB-2955        TCGA-AB-2956 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2959        TCGA-AB-2963        TCGA-AB-2964        TCGA-AB-2965 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2966        TCGA-AB-2967        TCGA-AB-2969        TCGA-AB-2970 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2971        TCGA-AB-2972        TCGA-AB-2973        TCGA-AB-2975 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2976        TCGA-AB-2977        TCGA-AB-2978        TCGA-AB-2979 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2980        TCGA-AB-2981        TCGA-AB-2982        TCGA-AB-2983 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" "PHACTR1 WILD-TYPE" 
D23V4, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     1   1
  PHACTR1 WILD-TYPE  56 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      1    1
  PHACTR1 WILD-TYPE   56  112
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  CLUS_1               1                56
  CLUS_2               1               112
D23V5, multiclass
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  CLUS_1               0                84
  CLUS_2               1                39
  CLUS_3               2                58
D23V6, multiclass
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  CLUS_1               1                37
  CLUS_2               0                81
  CLUS_3               2                63

Clustering(24) Variable = DIS3 MUTATION ANALYSIS
D24V1, multiclass
D24V2, multiclass
[1] "Remove cluster labels:" "DIS3 MUTATED"          
clus
  DIS3 MUTATED DIS3 WILD-TYPE 
             2            189 
    TCGA-AB-2802     TCGA-AB-2803     TCGA-AB-2804     TCGA-AB-2805 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2806     TCGA-AB-2807     TCGA-AB-2808     TCGA-AB-2809 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2810     TCGA-AB-2811     TCGA-AB-2812     TCGA-AB-2813 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2814     TCGA-AB-2816     TCGA-AB-2817     TCGA-AB-2818 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2819     TCGA-AB-2820     TCGA-AB-2821     TCGA-AB-2822 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2823     TCGA-AB-2824     TCGA-AB-2825     TCGA-AB-2826 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2827     TCGA-AB-2828     TCGA-AB-2829     TCGA-AB-2830 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2831     TCGA-AB-2832     TCGA-AB-2833     TCGA-AB-2834 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2835     TCGA-AB-2836     TCGA-AB-2837     TCGA-AB-2838 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2839     TCGA-AB-2840     TCGA-AB-2841     TCGA-AB-2842 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2843     TCGA-AB-2844     TCGA-AB-2845     TCGA-AB-2846 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2847     TCGA-AB-2848     TCGA-AB-2849     TCGA-AB-2851 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2853     TCGA-AB-2854     TCGA-AB-2855     TCGA-AB-2857 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2858     TCGA-AB-2860     TCGA-AB-2861     TCGA-AB-2862 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2863     TCGA-AB-2866     TCGA-AB-2867     TCGA-AB-2868 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2869     TCGA-AB-2870     TCGA-AB-2871     TCGA-AB-2872 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2873     TCGA-AB-2874     TCGA-AB-2875     TCGA-AB-2876 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2877     TCGA-AB-2878     TCGA-AB-2879     TCGA-AB-2880 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2881     TCGA-AB-2882     TCGA-AB-2883     TCGA-AB-2884 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2885     TCGA-AB-2886     TCGA-AB-2887     TCGA-AB-2888 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2889     TCGA-AB-2890     TCGA-AB-2891     TCGA-AB-2892 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2893     TCGA-AB-2894     TCGA-AB-2895     TCGA-AB-2896 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2897     TCGA-AB-2898     TCGA-AB-2899     TCGA-AB-2900 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2901     TCGA-AB-2903     TCGA-AB-2904     TCGA-AB-2906 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2907     TCGA-AB-2908     TCGA-AB-2909     TCGA-AB-2910 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2911     TCGA-AB-2912     TCGA-AB-2913     TCGA-AB-2914 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2915     TCGA-AB-2916     TCGA-AB-2917     TCGA-AB-2918 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2919     TCGA-AB-2920     TCGA-AB-2921     TCGA-AB-2922 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2923     TCGA-AB-2924     TCGA-AB-2925     TCGA-AB-2926 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2928     TCGA-AB-2929     TCGA-AB-2930     TCGA-AB-2931 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2932     TCGA-AB-2933     TCGA-AB-2934     TCGA-AB-2935 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2936     TCGA-AB-2937     TCGA-AB-2938     TCGA-AB-2939 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2940     TCGA-AB-2941     TCGA-AB-2942     TCGA-AB-2943 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2945     TCGA-AB-2946     TCGA-AB-2947     TCGA-AB-2948 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2949     TCGA-AB-2950     TCGA-AB-2952     TCGA-AB-2954 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2955     TCGA-AB-2956     TCGA-AB-2957     TCGA-AB-2959 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2963     TCGA-AB-2964     TCGA-AB-2965     TCGA-AB-2966 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2967     TCGA-AB-2968     TCGA-AB-2969     TCGA-AB-2970 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2971     TCGA-AB-2972     TCGA-AB-2973     TCGA-AB-2974 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2975     TCGA-AB-2976     TCGA-AB-2977     TCGA-AB-2978 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2979     TCGA-AB-2980     TCGA-AB-2981     TCGA-AB-2982 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2983     TCGA-AB-2984     TCGA-AB-2985     TCGA-AB-2986 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2987     TCGA-AB-2988     TCGA-AB-2989     TCGA-AB-2990 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2991     TCGA-AB-2992     TCGA-AB-2993     TCGA-AB-2995 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2996     TCGA-AB-2998     TCGA-AB-2999     TCGA-AB-3000 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-3001     TCGA-AB-3002     TCGA-AB-3005     TCGA-AB-3006 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-3007     TCGA-AB-3008     TCGA-AB-3009     TCGA-AB-3011 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-3012 
"DIS3 WILD-TYPE" 
D24V3, multiclass
[1] "Remove cluster labels:" "DIS3 MUTATED"          
clus
  DIS3 MUTATED DIS3 WILD-TYPE 
             2            168 
    TCGA-AB-2803     TCGA-AB-2805     TCGA-AB-2806     TCGA-AB-2807 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2808     TCGA-AB-2810     TCGA-AB-2811     TCGA-AB-2812 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2813     TCGA-AB-2814     TCGA-AB-2816     TCGA-AB-2817 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2818     TCGA-AB-2819     TCGA-AB-2820     TCGA-AB-2821 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2822     TCGA-AB-2823     TCGA-AB-2824     TCGA-AB-2825 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2826     TCGA-AB-2828     TCGA-AB-2830     TCGA-AB-2832 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2833     TCGA-AB-2834     TCGA-AB-2835     TCGA-AB-2836 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2837     TCGA-AB-2838     TCGA-AB-2839     TCGA-AB-2840 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2841     TCGA-AB-2842     TCGA-AB-2843     TCGA-AB-2844 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2845     TCGA-AB-2846     TCGA-AB-2847     TCGA-AB-2848 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2849     TCGA-AB-2851     TCGA-AB-2853     TCGA-AB-2854 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2855     TCGA-AB-2857     TCGA-AB-2858     TCGA-AB-2859 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2860     TCGA-AB-2861     TCGA-AB-2862     TCGA-AB-2863 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2866     TCGA-AB-2867     TCGA-AB-2868     TCGA-AB-2869 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2870     TCGA-AB-2871     TCGA-AB-2872     TCGA-AB-2873 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2874     TCGA-AB-2875     TCGA-AB-2877     TCGA-AB-2879 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2880     TCGA-AB-2881     TCGA-AB-2882     TCGA-AB-2884 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2885     TCGA-AB-2886     TCGA-AB-2887     TCGA-AB-2888 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2889     TCGA-AB-2890     TCGA-AB-2891     TCGA-AB-2895 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2896     TCGA-AB-2897     TCGA-AB-2898     TCGA-AB-2899 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2900     TCGA-AB-2901     TCGA-AB-2903     TCGA-AB-2904 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2908     TCGA-AB-2909     TCGA-AB-2910     TCGA-AB-2911 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2912     TCGA-AB-2913     TCGA-AB-2914     TCGA-AB-2915 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2916     TCGA-AB-2917     TCGA-AB-2918     TCGA-AB-2919 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2920     TCGA-AB-2921     TCGA-AB-2924     TCGA-AB-2925 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2928     TCGA-AB-2929     TCGA-AB-2930     TCGA-AB-2931 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2932     TCGA-AB-2933     TCGA-AB-2934     TCGA-AB-2935 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2936     TCGA-AB-2937     TCGA-AB-2938     TCGA-AB-2939 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2940     TCGA-AB-2941     TCGA-AB-2942     TCGA-AB-2943 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2946     TCGA-AB-2948     TCGA-AB-2949     TCGA-AB-2950 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2952     TCGA-AB-2954     TCGA-AB-2955     TCGA-AB-2956 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2959     TCGA-AB-2963     TCGA-AB-2964     TCGA-AB-2965 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2966     TCGA-AB-2967     TCGA-AB-2969     TCGA-AB-2970 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2971     TCGA-AB-2972     TCGA-AB-2973     TCGA-AB-2975 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2976     TCGA-AB-2977     TCGA-AB-2978     TCGA-AB-2979 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2980     TCGA-AB-2981     TCGA-AB-2982     TCGA-AB-2983 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2984     TCGA-AB-2985     TCGA-AB-2986     TCGA-AB-2987 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2988     TCGA-AB-2990     TCGA-AB-2991     TCGA-AB-2992 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2993     TCGA-AB-2994     TCGA-AB-2995     TCGA-AB-2996 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-2998     TCGA-AB-2999     TCGA-AB-3000     TCGA-AB-3001 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-3002     TCGA-AB-3005     TCGA-AB-3006     TCGA-AB-3007 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
    TCGA-AB-3008     TCGA-AB-3009     TCGA-AB-3011     TCGA-AB-3012 
"DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" "DIS3 WILD-TYPE" 
D24V4, binary
                cls
clus               0   1
  DIS3 MUTATED     1   1
  DIS3 WILD-TYPE  56 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  DIS3 MUTATED      1    1
  DIS3 WILD-TYPE   56  112
        clus
vv       DIS3 MUTATED DIS3 WILD-TYPE
  CLUS_1            1             56
  CLUS_2            1            112
D24V5, multiclass
        clus
vv       DIS3 MUTATED DIS3 WILD-TYPE
  CLUS_1            0             84
  CLUS_2            2             38
  CLUS_3            1             59
D24V6, multiclass
        clus
vv       DIS3 MUTATED DIS3 WILD-TYPE
  CLUS_1            2             36
  CLUS_2            0             81
  CLUS_3            1             64
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
