
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/8209187/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/8282702/PRAD-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ALL", "-oT=PRAD-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=PRAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PRAD-TP/8282702/PRAD-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/8209187/transformed.cor.cli.txt"

nPatients in clinical file=336, in cluster file=261, common to both=261
[1]  10 261
[1] "KIDINS220 MUTATION ANALYSIS"
[1] 3
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                  3                 258 
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                  3                 258 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              252 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               9              252 
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            26            235 
  SPOP MUTATED SPOP WILD-TYPE 
            26            235 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            23            238 
  TP53 MUTATED TP53 WILD-TYPE 
            23            238 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            13            248 
  PTEN MUTATED PTEN WILD-TYPE 
            13            248 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             12             249 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             12             249 
[1] "LMOD2 MUTATION ANALYSIS"
[1] 3
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              3             258 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              3             258 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            257 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            257 
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              256 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              256 
[1] "CDKN1B MUTATION ANALYSIS"
[1] 3
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               4              257 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               4              257 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 261 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:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 261 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, 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=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KIDINS220 MUTATION ANALYSIS
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  KIDINS220 MUTATED        0      1      2
  KIDINS220 WILD-TYPE     35    143     77
D1V1, multiclass
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  CLUS_1                 0                  35
  CLUS_2                 1                 143
  CLUS_3                 2                  77
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  KIDINS220 MUTATED        1      2      0
  KIDINS220 WILD-TYPE     74     87     97
D1V2, multiclass
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  CLUS_1                 1                  74
  CLUS_2                 2                  87
  CLUS_3                 0                  97
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  KIDINS220 MUTATED        1      1      0
  KIDINS220 WILD-TYPE     41     58     63
D1V3, multiclass
[1] "Remove cluster labels:" "KIDINS220 MUTATED"     
clus
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                  2                 162 
         TCGA-CH-5737          TCGA-CH-5738          TCGA-CH-5739 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5740          TCGA-CH-5741          TCGA-CH-5743 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5744          TCGA-CH-5745          TCGA-CH-5748 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5750          TCGA-CH-5751          TCGA-CH-5752 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5753          TCGA-CH-5754          TCGA-CH-5761 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5763          TCGA-CH-5764          TCGA-CH-5765 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5766          TCGA-CH-5767          TCGA-CH-5768 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5769          TCGA-CH-5771          TCGA-CH-5772 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5788          TCGA-CH-5789          TCGA-CH-5790 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5791          TCGA-CH-5792          TCGA-CH-5794 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5494          TCGA-EJ-5495          TCGA-EJ-5496 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5497          TCGA-EJ-5498          TCGA-EJ-5499 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5501          TCGA-EJ-5502          TCGA-EJ-5503 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5504          TCGA-EJ-5505          TCGA-EJ-5506 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5507          TCGA-EJ-5508          TCGA-EJ-5509 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5510          TCGA-EJ-5511          TCGA-EJ-5512 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5514          TCGA-EJ-5515          TCGA-EJ-5516 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5517          TCGA-EJ-5518          TCGA-EJ-5519 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5521          TCGA-EJ-5522          TCGA-EJ-5524 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5525          TCGA-EJ-5526          TCGA-EJ-5527 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5530          TCGA-EJ-5531          TCGA-EJ-5532 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5542          TCGA-EJ-7115          TCGA-EJ-7125 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7314          TCGA-EJ-7317          TCGA-EJ-7321 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7328          TCGA-EJ-7330          TCGA-EJ-7331 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7781          TCGA-EJ-7782          TCGA-EJ-7783 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7784          TCGA-EJ-7785          TCGA-EJ-7786 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7788          TCGA-EJ-7789          TCGA-EJ-7791 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7792          TCGA-EJ-7793          TCGA-EJ-7794 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7797          TCGA-EJ-8468          TCGA-EJ-8469 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-8470          TCGA-EJ-8474          TCGA-EJ-A46B 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-A46D          TCGA-EJ-A46E          TCGA-EJ-A46F 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-A46G          TCGA-EJ-A65E          TCGA-EJ-A65M 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-FC-7708          TCGA-FC-7961          TCGA-FC-A4JI 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-FC-A5OB          TCGA-G9-6329          TCGA-G9-6338 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6342          TCGA-G9-6343          TCGA-G9-6351 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6353          TCGA-G9-6356          TCGA-G9-6361 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6362          TCGA-G9-6363          TCGA-G9-6364 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6365          TCGA-G9-6366          TCGA-G9-6367 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6370          TCGA-G9-6371          TCGA-G9-6373 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6377          TCGA-G9-6378          TCGA-G9-6384 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6494          TCGA-G9-6496          TCGA-G9-6499 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-7510          TCGA-G9-7521          TCGA-G9-7522 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-7523          TCGA-G9-7525          TCGA-H9-7775 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7077          TCGA-HC-7079          TCGA-HC-7081 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7210          TCGA-HC-7211          TCGA-HC-7212 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7213          TCGA-HC-7232          TCGA-HC-7233 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7736          TCGA-HC-7740          TCGA-HC-7744 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7748          TCGA-HC-7817          TCGA-HC-8264 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HI-7168          TCGA-HI-7169          TCGA-HI-7170 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HI-7171          TCGA-J4-8198          TCGA-J4-8200 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-J9-A52C          TCGA-J9-A52E          TCGA-KC-A4BL 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-KC-A4BN          TCGA-KC-A4BO          TCGA-KC-A4BR 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-KC-A4BV          TCGA-KK-A59V          TCGA-KK-A59X 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-KK-A59Y          TCGA-KK-A59Z          TCGA-KK-A5A1 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  KIDINS220 MUTATED        1      0      1
  KIDINS220 WILD-TYPE     51     64     47
D1V4, multiclass
[1] "Remove cluster labels:" "KIDINS220 MUTATED"     
clus
  KIDINS220 MUTATED KIDINS220 WILD-TYPE 
                  2                 162 
         TCGA-CH-5737          TCGA-CH-5738          TCGA-CH-5739 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5740          TCGA-CH-5741          TCGA-CH-5743 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5744          TCGA-CH-5745          TCGA-CH-5748 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5750          TCGA-CH-5751          TCGA-CH-5752 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5753          TCGA-CH-5754          TCGA-CH-5761 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5763          TCGA-CH-5764          TCGA-CH-5765 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5766          TCGA-CH-5767          TCGA-CH-5768 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5769          TCGA-CH-5771          TCGA-CH-5772 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5788          TCGA-CH-5789          TCGA-CH-5790 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-CH-5791          TCGA-CH-5792          TCGA-CH-5794 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5494          TCGA-EJ-5495          TCGA-EJ-5496 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5497          TCGA-EJ-5498          TCGA-EJ-5499 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5501          TCGA-EJ-5502          TCGA-EJ-5503 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5504          TCGA-EJ-5505          TCGA-EJ-5506 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5507          TCGA-EJ-5508          TCGA-EJ-5509 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5510          TCGA-EJ-5511          TCGA-EJ-5512 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5514          TCGA-EJ-5515          TCGA-EJ-5516 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5517          TCGA-EJ-5518          TCGA-EJ-5519 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5521          TCGA-EJ-5522          TCGA-EJ-5524 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5525          TCGA-EJ-5526          TCGA-EJ-5527 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5530          TCGA-EJ-5531          TCGA-EJ-5532 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-5542          TCGA-EJ-7115          TCGA-EJ-7125 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7314          TCGA-EJ-7317          TCGA-EJ-7321 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7328          TCGA-EJ-7330          TCGA-EJ-7331 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7781          TCGA-EJ-7782          TCGA-EJ-7783 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7784          TCGA-EJ-7785          TCGA-EJ-7786 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7788          TCGA-EJ-7789          TCGA-EJ-7791 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7792          TCGA-EJ-7793          TCGA-EJ-7794 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-7797          TCGA-EJ-8468          TCGA-EJ-8469 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-8470          TCGA-EJ-8474          TCGA-EJ-A46B 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-A46D          TCGA-EJ-A46E          TCGA-EJ-A46F 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-EJ-A46G          TCGA-EJ-A65E          TCGA-EJ-A65M 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-FC-7708          TCGA-FC-7961          TCGA-FC-A4JI 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-FC-A5OB          TCGA-G9-6329          TCGA-G9-6338 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6342          TCGA-G9-6343          TCGA-G9-6351 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6353          TCGA-G9-6356          TCGA-G9-6361 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6362          TCGA-G9-6363          TCGA-G9-6364 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6365          TCGA-G9-6366          TCGA-G9-6367 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6370          TCGA-G9-6371          TCGA-G9-6373 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6377          TCGA-G9-6378          TCGA-G9-6384 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-6494          TCGA-G9-6496          TCGA-G9-6499 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-7510          TCGA-G9-7521          TCGA-G9-7522 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-G9-7523          TCGA-G9-7525          TCGA-H9-7775 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7077          TCGA-HC-7079          TCGA-HC-7081 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7210          TCGA-HC-7211          TCGA-HC-7212 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7213          TCGA-HC-7232          TCGA-HC-7233 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7736          TCGA-HC-7740          TCGA-HC-7744 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HC-7748          TCGA-HC-7817          TCGA-HC-8264 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HI-7168          TCGA-HI-7169          TCGA-HI-7170 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-HI-7171          TCGA-J4-8198          TCGA-J4-8200 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-J9-A52C          TCGA-J9-A52E          TCGA-KC-A4BL 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-KC-A4BN          TCGA-KC-A4BO          TCGA-KC-A4BR 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-KC-A4BV          TCGA-KK-A59V          TCGA-KK-A59X 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
         TCGA-KK-A59Y          TCGA-KK-A59Z          TCGA-KK-A5A1 
"KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" "KIDINS220 WILD-TYPE" 
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  KIDINS220 MUTATED        1      1      1
  KIDINS220 WILD-TYPE     88     80     87
D1V5, multiclass
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  CLUS_1                 1                  88
  CLUS_2                 1                  80
  CLUS_3                 1                  87
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3
  KIDINS220 MUTATED        1      1      1
  KIDINS220 WILD-TYPE     82     83     90
D1V6, multiclass
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  CLUS_1                 1                  82
  CLUS_2                 1                  83
  CLUS_3                 1                  90
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIDINS220 MUTATED        1      1      1      0      0
  KIDINS220 WILD-TYPE     62     38     79     16     61
D1V7, multiclass
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIDINS220 MUTATED        0      1      1      1
  KIDINS220 WILD-TYPE     43     53     88     72
D1V8, multiclass
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  CLUS_1                 0                  43
  CLUS_2                 1                  53
  CLUS_3                 1                  88
  CLUS_4                 1                  72
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  KIDINS220 MUTATED        1      0      1      1      0
  KIDINS220 WILD-TYPE     80     16     84     58     18
D1V9, multiclass
                     vv
clus                  CLUS_1 CLUS_2 CLUS_3 CLUS_4
  KIDINS220 MUTATED        1      0      1      1
  KIDINS220 WILD-TYPE     66     32     77     81
D1V10, multiclass
        clus
vv       KIDINS220 MUTATED KIDINS220 WILD-TYPE
  CLUS_1                 1                  66
  CLUS_2                 0                  32
  CLUS_3                 1                  77
  CLUS_4                 1                  81

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      2      4
  CTNNB1 WILD-TYPE     32    142     75
D2V1, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               32
  CLUS_2              2              142
  CLUS_3              4               75
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      0      6
  CTNNB1 WILD-TYPE     72     89     91
D2V2, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               72
  CLUS_2              0               89
  CLUS_3              6               91
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        0      0      4
  CTNNB1 WILD-TYPE     42     59     59
D2V3, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               42
  CLUS_2              0               59
  CLUS_3              4               59
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        0      4      0
  CTNNB1 WILD-TYPE     52     60     48
D2V4, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               52
  CLUS_2              4               60
  CLUS_3              0               48
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        4      0      5
  CTNNB1 WILD-TYPE     85     81     83
D2V5, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              4               85
  CLUS_2              0               81
  CLUS_3              5               83
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CTNNB1 MUTATED        3      1      5
  CTNNB1 WILD-TYPE     80     83     86
D2V6, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              3               80
  CLUS_2              1               83
  CLUS_3              5               86
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        2      0      3      0      4
  CTNNB1 WILD-TYPE     61     39     77     16     57
D2V7, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        0      4      3      2
  CTNNB1 WILD-TYPE     43     50     86     71
D2V8, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              0               43
  CLUS_2              4               50
  CLUS_3              3               86
  CLUS_4              2               71
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CTNNB1 MUTATED        3      1      2      3      0
  CTNNB1 WILD-TYPE     78     15     83     56     18
D2V9, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CTNNB1 MUTATED        2      0      2      5
  CTNNB1 WILD-TYPE     65     32     76     77
D2V10, multiclass
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  CLUS_1              2               65
  CLUS_2              0               32
  CLUS_3              2               76
  CLUS_4              5               77

Clustering(3) Variable = SPOP MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       10      6      9
  SPOP WILD-TYPE     25    138     70
D3V1, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           10             25
  CLUS_2            6            138
  CLUS_3            9             70
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       21      4      1
  SPOP WILD-TYPE     54     85     96
D3V2, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           21             54
  CLUS_2            4             85
  CLUS_3            1             96
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED        4      3      8
  SPOP WILD-TYPE     38     56     55
D3V3, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            4             38
  CLUS_2            3             56
  CLUS_3            8             55
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED        5      7      3
  SPOP WILD-TYPE     47     57     45
D3V4, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            5             47
  CLUS_2            7             57
  CLUS_3            3             45
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       17      7      1
  SPOP WILD-TYPE     72     74     87
D3V5, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           17             72
  CLUS_2            7             74
  CLUS_3            1             87
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  SPOP MUTATED       20      4      1
  SPOP WILD-TYPE     63     80     90
D3V6, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1           20             63
  CLUS_2            4             80
  CLUS_3            1             90
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SPOP MUTATED        4      4     10      0      8
  SPOP WILD-TYPE     59     35     70     16     53
D3V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SPOP MUTATED        3      6      9      8
  SPOP WILD-TYPE     40     48     80     65
D3V8, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             40
  CLUS_2            6             48
  CLUS_3            9             80
  CLUS_4            8             65
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  SPOP MUTATED        4      0     10      9      3
  SPOP WILD-TYPE     77     16     75     50     15
D3V9, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  SPOP MUTATED        3      1     11     11
  SPOP WILD-TYPE     64     31     67     71
D3V10, multiclass
        clus
vv       SPOP MUTATED SPOP WILD-TYPE
  CLUS_1            3             64
  CLUS_2            1             31
  CLUS_3           11             67
  CLUS_4           11             71

Clustering(4) Variable = TP53 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        0      4     19
  TP53 WILD-TYPE     35    140     60
D4V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             35
  CLUS_2            4            140
  CLUS_3           19             60
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        6      5     12
  TP53 WILD-TYPE     69     84     85
D4V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             69
  CLUS_2            5             84
  CLUS_3           12             85
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        0      3     10
  TP53 WILD-TYPE     42     56     53
D4V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            3             56
  CLUS_3           10             53
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        1     10      2
  TP53 WILD-TYPE     51     54     46
D4V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             51
  CLUS_2           10             54
  CLUS_3            2             46
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        6      3     14
  TP53 WILD-TYPE     83     78     74
D4V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6             83
  CLUS_2            3             78
  CLUS_3           14             74
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  TP53 MUTATED        4      2     17
  TP53 WILD-TYPE     79     82     74
D4V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             79
  CLUS_2            2             82
  CLUS_3           17             74
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        5      2      9      1      6
  TP53 WILD-TYPE     58     37     71     15     55
D4V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        2      7      6      8
  TP53 WILD-TYPE     41     47     83     65
D4V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             41
  CLUS_2            7             47
  CLUS_3            6             83
  CLUS_4            8             65
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  TP53 MUTATED        5      0     11      6      1
  TP53 WILD-TYPE     76     16     74     53     17
D4V9, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  TP53 MUTATED        4      2     10      7
  TP53 WILD-TYPE     63     30     68     75
D4V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             63
  CLUS_2            2             30
  CLUS_3           10             68
  CLUS_4            7             75

Clustering(5) Variable = PTEN MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        3      3      7
  PTEN WILD-TYPE     32    141     72
D5V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             32
  CLUS_2            3            141
  CLUS_3            7             72
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        4      2      7
  PTEN WILD-TYPE     71     87     90
D5V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             71
  CLUS_2            2             87
  CLUS_3            7             90
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        4      1      3
  PTEN WILD-TYPE     38     58     60
D5V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             38
  CLUS_2            1             58
  CLUS_3            3             60
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        4      2      2
  PTEN WILD-TYPE     48     62     46
D5V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             48
  CLUS_2            2             62
  CLUS_3            2             46
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        6      1      6
  PTEN WILD-TYPE     83     80     82
D5V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            6             83
  CLUS_2            1             80
  CLUS_3            6             82
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  PTEN MUTATED        4      1      8
  PTEN WILD-TYPE     79     83     83
D5V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             79
  CLUS_2            1             83
  CLUS_3            8             83
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        3      0      3      1      6
  PTEN WILD-TYPE     60     39     77     15     55
D5V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        1      6      2      4
  PTEN WILD-TYPE     42     48     87     69
D5V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             42
  CLUS_2            6             48
  CLUS_3            2             87
  CLUS_4            4             69
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  PTEN MUTATED        3      1      3      6      0
  PTEN WILD-TYPE     78     15     82     53     18
D5V9, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  PTEN MUTATED        3      0      4      6
  PTEN WILD-TYPE     64     32     74     76
D5V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             64
  CLUS_2            0             32
  CLUS_3            4             74
  CLUS_4            6             76

Clustering(6) Variable = FOXA1 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        5      4      3
  FOXA1 WILD-TYPE     30    140     76
D6V1, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             5              30
  CLUS_2             4             140
  CLUS_3             3              76
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED       10      1      1
  FOXA1 WILD-TYPE     65     88     96
D6V2, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1            10              65
  CLUS_2             1              88
  CLUS_3             1              96
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        2      2      3
  FOXA1 WILD-TYPE     40     57     60
D6V3, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             2              40
  CLUS_2             2              57
  CLUS_3             3              60
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        3      3      1
  FOXA1 WILD-TYPE     49     61     47
D6V4, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             3              49
  CLUS_2             3              61
  CLUS_3             1              47
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        8      3      1
  FOXA1 WILD-TYPE     81     78     87
D6V5, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             8              81
  CLUS_2             3              78
  CLUS_3             1              87
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  FOXA1 MUTATED        8      2      2
  FOXA1 WILD-TYPE     75     82     89
D6V6, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             8              75
  CLUS_2             2              82
  CLUS_3             2              89
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FOXA1 MUTATED        1      1      6      0      4
  FOXA1 WILD-TYPE     62     38     74     16     57
D6V7, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXA1 MUTATED        1      5      1      5
  FOXA1 WILD-TYPE     42     49     88     68
D6V8, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             1              42
  CLUS_2             5              49
  CLUS_3             1              88
  CLUS_4             5              68
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  FOXA1 MUTATED        1      1      6      3      1
  FOXA1 WILD-TYPE     80     15     79     56     17
D6V9, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  FOXA1 MUTATED        1      0      5      6
  FOXA1 WILD-TYPE     66     32     73     76
D6V10, multiclass
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  CLUS_1             1              66
  CLUS_2             0              32
  CLUS_3             5              73
  CLUS_4             6              76

Clustering(7) Variable = LMOD2 MUTATION ANALYSIS
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      2      1
  LMOD2 WILD-TYPE     35    142     78
D7V1, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             0              35
  CLUS_2             2             142
  CLUS_3             1              78
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      2      1
  LMOD2 WILD-TYPE     75     87     96
D7V2, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             0              75
  CLUS_2             2              87
  CLUS_3             1              96
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      1      1
  LMOD2 WILD-TYPE     42     58     62
D7V3, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7328 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8469      TCGA-EJ-8470      TCGA-EJ-8474      TCGA-EJ-A46D 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7525      TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        0      1      1
  LMOD2 WILD-TYPE     52     63     47
D7V4, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              2             162 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7328 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-8469      TCGA-EJ-8470      TCGA-EJ-8474      TCGA-EJ-A46D 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-FC-7708      TCGA-FC-7961      TCGA-FC-A4JI 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-G9-6329      TCGA-G9-6338      TCGA-G9-6342 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-7525      TCGA-H9-7775      TCGA-HC-7077      TCGA-HC-7079 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7748      TCGA-HC-7817      TCGA-HC-8264 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J9-A52C      TCGA-J9-A52E 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-KK-A59Z      TCGA-KK-A5A1 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        1      1      1
  LMOD2 WILD-TYPE     88     80     87
D7V5, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              88
  CLUS_2             1              80
  CLUS_3             1              87
                 vv
clus              CLUS_1 CLUS_2 CLUS_3
  LMOD2 MUTATED        1      1      1
  LMOD2 WILD-TYPE     82     83     90
D7V6, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              82
  CLUS_2             1              83
  CLUS_3             1              90
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LMOD2 MUTATED        0      1      1      0      1
  LMOD2 WILD-TYPE     63     38     79     16     60
D7V7, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LMOD2 MUTATED        1      0      1      1
  LMOD2 WILD-TYPE     42     54     88     72
D7V8, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             1              42
  CLUS_2             0              54
  CLUS_3             1              88
  CLUS_4             1              72
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  LMOD2 MUTATED        0      1      1      0      1
  LMOD2 WILD-TYPE     81     15     84     59     17
D7V9, multiclass
                 vv
clus              CLUS_1 CLUS_2 CLUS_3 CLUS_4
  LMOD2 MUTATED        0      1      1      1
  LMOD2 WILD-TYPE     67     31     77     81
D7V10, multiclass
        clus
vv       LMOD2 MUTATED LMOD2 WILD-TYPE
  CLUS_1             0              67
  CLUS_2             1              31
  CLUS_3             1              77
  CLUS_4             1              81

Clustering(8) Variable = IDH1 MUTATION ANALYSIS
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        2      1      1
  IDH1 WILD-TYPE     33    143     78
D8V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            2             33
  CLUS_2            1            143
  CLUS_3            1             78
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        4      0      0
  IDH1 WILD-TYPE     71     89     97
D8V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             71
  CLUS_2            0             89
  CLUS_3            0             97
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        0      3      0
  IDH1 WILD-TYPE     42     56     63
D8V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             42
  CLUS_2            3             56
  CLUS_3            0             63
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        0      0      3
  IDH1 WILD-TYPE     52     64     45
D8V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             52
  CLUS_2            0             64
  CLUS_3            3             45
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        4      0      0
  IDH1 WILD-TYPE     85     81     88
D8V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             85
  CLUS_2            0             81
  CLUS_3            0             88
                vv
clus             CLUS_1 CLUS_2 CLUS_3
  IDH1 MUTATED        4      0      0
  IDH1 WILD-TYPE     79     84     91
D8V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            4             79
  CLUS_2            0             84
  CLUS_3            0             91
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDH1 MUTATED        0      0      1      2      1
  IDH1 WILD-TYPE     63     39     79     14     60
D8V7, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        3      1      0      0
  IDH1 WILD-TYPE     40     53     89     73
D8V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             40
  CLUS_2            1             53
  CLUS_3            0             89
  CLUS_4            0             73
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  IDH1 MUTATED        0      2      1      1      0
  IDH1 WILD-TYPE     81     14     84     58     18
D8V9, multiclass
                vv
clus             CLUS_1 CLUS_2 CLUS_3 CLUS_4
  IDH1 MUTATED        0      2      1      1
  IDH1 WILD-TYPE     67     30     77     81
D8V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             67
  CLUS_2            2             30
  CLUS_3            1             77
  CLUS_4            1             81

Clustering(9) Variable = NKX3-1 MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        1      3      0
  NKX3-1 WILD-TYPE     34    141     79
D9V1, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              1               34
  CLUS_2              3              141
  CLUS_3              0               79
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        1      1      3
  NKX3-1 WILD-TYPE     74     88     94
D9V2, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              1               74
  CLUS_2              1               88
  CLUS_3              3               94
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        4      0      1
  NKX3-1 WILD-TYPE     38     59     62
D9V3, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              4               38
  CLUS_2              0               59
  CLUS_3              1               62
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        4      1      0
  NKX3-1 WILD-TYPE     48     63     48
D9V4, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              4               48
  CLUS_2              1               63
  CLUS_3              0               48
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        2      1      2
  NKX3-1 WILD-TYPE     87     80     86
D9V5, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               87
  CLUS_2              1               80
  CLUS_3              2               86
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  NKX3-1 MUTATED        2      1      2
  NKX3-1 WILD-TYPE     81     83     89
D9V6, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               81
  CLUS_2              1               83
  CLUS_3              2               89
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NKX3-1 MUTATED        4      0      0      1      0
  NKX3-1 WILD-TYPE     59     39     80     15     61
D9V7, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NKX3-1 MUTATED        2      0      2      1
  NKX3-1 WILD-TYPE     41     54     87     72
D9V8, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              2               41
  CLUS_2              0               54
  CLUS_3              2               87
  CLUS_4              1               72
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  NKX3-1 MUTATED        5      0      0      0      0
  NKX3-1 WILD-TYPE     76     16     85     59     18
D9V9, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  NKX3-1 MUTATED        3      2      0      0
  NKX3-1 WILD-TYPE     64     30     78     82
D9V10, multiclass
        clus
vv       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  CLUS_1              3               64
  CLUS_2              2               30
  CLUS_3              0               78
  CLUS_4              0               82

Clustering(10) Variable = CDKN1B MUTATION ANALYSIS
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        2      1      1
  CDKN1B WILD-TYPE     33    143     78
D10V1, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              2               33
  CLUS_2              1              143
  CLUS_3              1               78
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        3      0      1
  CDKN1B WILD-TYPE     72     89     96
D10V2, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              3               72
  CLUS_2              0               89
  CLUS_3              1               96
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        1      0      3
  CDKN1B WILD-TYPE     41     59     60
D10V3, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              1               41
  CLUS_2              0               59
  CLUS_3              3               60
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        1      3      0
  CDKN1B WILD-TYPE     51     61     48
D10V4, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              1               51
  CLUS_2              3               61
  CLUS_3              0               48
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        3      0      1
  CDKN1B WILD-TYPE     86     81     87
D10V5, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              3               86
  CLUS_2              0               81
  CLUS_3              1               87
                  vv
clus               CLUS_1 CLUS_2 CLUS_3
  CDKN1B MUTATED        1      0      3
  CDKN1B WILD-TYPE     82     84     88
D10V6, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              1               82
  CLUS_2              0               84
  CLUS_3              3               88
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN1B MUTATED        2      0      1      0      1
  CDKN1B WILD-TYPE     61     39     79     16     60
D10V7, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN1B MUTATED        2      2      0      0
  CDKN1B WILD-TYPE     41     52     89     73
D10V8, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              2               41
  CLUS_2              2               52
  CLUS_3              0               89
  CLUS_4              0               73
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  CDKN1B MUTATED        2      0      1      1      0
  CDKN1B WILD-TYPE     79     16     84     58     18
D10V9, multiclass
                  vv
clus               CLUS_1 CLUS_2 CLUS_3 CLUS_4
  CDKN1B MUTATED        1      2      0      1
  CDKN1B WILD-TYPE     66     30     78     81
D10V10, multiclass
        clus
vv       CDKN1B MUTATED CDKN1B WILD-TYPE
  CLUS_1              1               66
  CLUS_2              2               30
  CLUS_3              0               78
  CLUS_4              1               81
> q(save="no")
