
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_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/335360/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRC-TP/2666908/1.GDAC_mergedClustering.Finished/KIRC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KIRC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=502, in cluster file=493, common to both=493
[1] "Reduce the number of clustering variables from 80 to 71."
[1]  71 493
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5               488 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5               488 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               461 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               461 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               48               445 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               48               445 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               49               444 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               49               444 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7               486 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7               486 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               27               466 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               27               466 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               485 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               485 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               485 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               485 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              141               352 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              141               352 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              156               337 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              156               337 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6               487 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6               487 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               488 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               488 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              127               366 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              127               366 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              129               364 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              129               364 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14               479 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14               479 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34               459 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34               459 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               485 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8               485 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               485 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                8               485 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                487 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                487 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                489 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                489 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                476 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                476 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                478 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                478 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                78                415 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                78                415 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                78                415 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                78                415 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                479 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                479 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                488 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                488 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                479 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                479 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                65                428 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                65                428 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                58                435 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                58                435 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                477 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                477 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                471 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                471 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                475 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                18                475 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                475 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                475 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                25                468 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                25                468 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                465 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                28                465 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                66                427 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                66                427 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                68                425 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                68                425 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                33                460 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                33                460 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                25                468 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                25                468 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11               482 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11               482 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               461 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               461 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               472 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               21               472 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               483 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               483 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               482 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               482 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              304               189 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              304               189 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               73               420 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               73               420 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35               458 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               35               458 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               28               465 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               28               465 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               58               435 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               58               435 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               82               411 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               82               411 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               94               399 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               94               399 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               37               456 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               37               456 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               87               406 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               87               406 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92               401 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92               401 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                461 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                461 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                48                445 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                48                445 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                488 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                488 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                486 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                486 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                31                462 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                31                462 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               158                335 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               158                335 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                481 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                481 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                488 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                488 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                25                468 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                25                468 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                481 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                481 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                46                447 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                46                447 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                445 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                48                445 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                489 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                489 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                487 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                487 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                461 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                461 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                482 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                11                482 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7               486 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7               486 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 

Input Data has 10 rows and 493 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 493 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
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=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3374 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3456 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V2, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3374 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3456 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               130
  CLUS_2               1               196
  CLUS_3               2               162
D1V4, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1               277 
       TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3367        TCGA-A3-3370 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-3373        TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3425        TCGA-AK-3428        TCGA-AK-3431        TCGA-AK-3433 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3434        TCGA-AK-3440        TCGA-AK-3445        TCGA-AK-3450 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3453        TCGA-AK-3454        TCGA-AK-3458        TCGA-AK-3460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3461        TCGA-B0-4688        TCGA-B0-4690        TCGA-B0-4691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4693        TCGA-B0-4694        TCGA-B0-4696        TCGA-B0-4697 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4698        TCGA-B0-4699        TCGA-B0-4700        TCGA-B0-4701 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4703        TCGA-B0-4706        TCGA-B0-4707        TCGA-B0-4710 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4712        TCGA-B0-4713        TCGA-B0-4714        TCGA-B0-4718 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4813        TCGA-B0-4814 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4815        TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4819        TCGA-B0-4821        TCGA-B0-4822        TCGA-B0-4823 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4824        TCGA-B0-4827        TCGA-B0-4828        TCGA-B0-4841 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4842        TCGA-B0-4843        TCGA-B0-4844        TCGA-B0-4845 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4846        TCGA-B0-4847        TCGA-B0-4848        TCGA-B0-4849 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-4852        TCGA-B0-4945        TCGA-B0-5080        TCGA-B0-5092 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5094        TCGA-B0-5095        TCGA-B0-5096        TCGA-B0-5097 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5098        TCGA-B0-5099        TCGA-B0-5100        TCGA-B0-5102 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107        TCGA-B0-5108 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5110        TCGA-B0-5113        TCGA-B0-5115        TCGA-B0-5116 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5117        TCGA-B0-5119        TCGA-B0-5120        TCGA-B0-5121 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5402        TCGA-B0-5690 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5693        TCGA-B0-5694 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5709        TCGA-B0-5710 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B0-5711        TCGA-B0-5712        TCGA-B0-5713        TCGA-B0-5812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-4101        TCGA-B2-5633        TCGA-B2-5635        TCGA-B2-5639 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5378        TCGA-B4-5832 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4146        TCGA-B8-4153 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5162        TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5545        TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5551        TCGA-B8-5552        TCGA-B8-5553        TCGA-BP-4177 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4760        TCGA-BP-4770        TCGA-BP-4782        TCGA-BP-4795 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-4801        TCGA-BP-4993        TCGA-BP-5010        TCGA-BP-5168 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5169        TCGA-BP-5170        TCGA-BP-5173        TCGA-BP-5174 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5175        TCGA-BP-5176        TCGA-BP-5177        TCGA-BP-5178 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5180        TCGA-BP-5181        TCGA-BP-5182        TCGA-BP-5183 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5184        TCGA-BP-5185        TCGA-BP-5186        TCGA-BP-5187 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5189        TCGA-BP-5190        TCGA-BP-5191        TCGA-BP-5192 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5194        TCGA-BP-5195        TCGA-BP-5196        TCGA-BP-5198 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BP-5199        TCGA-BP-5200        TCGA-BP-5201        TCGA-BP-5202 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4869        TCGA-CJ-4882        TCGA-CJ-4897        TCGA-CJ-4901 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4902        TCGA-CJ-4903        TCGA-CJ-4904        TCGA-CJ-4905 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4907        TCGA-CJ-4908        TCGA-CJ-4912        TCGA-CJ-4913 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-4916        TCGA-CJ-4918        TCGA-CJ-4920        TCGA-CJ-4923 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5671        TCGA-CJ-5672        TCGA-CJ-5675        TCGA-CJ-5676 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5677        TCGA-CJ-5678        TCGA-CJ-5679        TCGA-CJ-5680 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5681        TCGA-CJ-5682        TCGA-CJ-5683        TCGA-CJ-5684 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-5686        TCGA-CJ-5689        TCGA-CJ-6027        TCGA-CJ-6028 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CJ-6030        TCGA-CJ-6031        TCGA-CJ-6032        TCGA-CJ-6033 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5580        TCGA-CW-5581        TCGA-CW-5583        TCGA-CW-5584 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5585        TCGA-CW-5587        TCGA-CW-5588        TCGA-CW-5589 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-5591        TCGA-CW-6087        TCGA-CW-6088        TCGA-CW-6090 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CW-6093        TCGA-CW-6097        TCGA-CZ-4853        TCGA-CZ-4856 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-4864        TCGA-CZ-4865 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-4866        TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5453 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5454        TCGA-CZ-5455        TCGA-CZ-5456        TCGA-CZ-5457 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5459        TCGA-CZ-5460        TCGA-CZ-5461 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5462        TCGA-CZ-5463        TCGA-CZ-5464        TCGA-CZ-5465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5466        TCGA-CZ-5467        TCGA-CZ-5468        TCGA-CZ-5469 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5470        TCGA-CZ-5982        TCGA-CZ-5984        TCGA-CZ-5985 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CZ-5986        TCGA-CZ-5987        TCGA-CZ-5988        TCGA-CZ-5989 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5567        TCGA-DV-5568 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5573        TCGA-DV-5574        TCGA-DV-5575 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EU-5907 
"1P GAIN WILD-TYPE" 
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               157
  CLUS_2               1               146
  CLUS_3               1               140
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               211
  CLUS_3               3               101
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               194
  CLUS_2               1               178
  CLUS_3               1                96
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                68
  CLUS_2               2               212
  CLUS_3               2               188
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               2               182
  CLUS_3               3               140
  CLUS_4               0                44
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               3               256
  CLUS_3               0                51

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                30
  CLUS_2               4                20
  CLUS_3               1                12
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                20
  CLUS_3               4                29
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              21               111
  CLUS_2               6               191
  CLUS_3               5               159
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8                88
  CLUS_2               5               113
  CLUS_3               3                61
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15               144
  CLUS_2               7               140
  CLUS_3               6               135
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              13               119
  CLUS_2               9               202
  CLUS_3               6                98
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              12               185
  CLUS_2              18               161
  CLUS_3               1                96
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                68
  CLUS_2              15               199
  CLUS_3              15               175
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               9               175
  CLUS_3              16               127
  CLUS_4               3                41
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              10               155
  CLUS_2              16               243
  CLUS_3               4                47

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4                29
  CLUS_2               2                22
  CLUS_3               0                13
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                21
  CLUS_3               4                29
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              29               103
  CLUS_2               9               188
  CLUS_3              10               154
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              10                86
  CLUS_2              10               108
  CLUS_3               4                60
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              16               143
  CLUS_2              14               133
  CLUS_3              12               129
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              12               120
  CLUS_2              21               190
  CLUS_3               9                95
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              24               173
  CLUS_2              16               163
  CLUS_3               5                92
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2              25               189
  CLUS_3              18               172
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               7                97
  CLUS_2              23               161
  CLUS_3              14               129
  CLUS_4               4                40
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              14               151
  CLUS_2              31               228
  CLUS_3               3                48

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                29
  CLUS_2               2                22
  CLUS_3               0                13
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                21
  CLUS_3               4                29
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              27               105
  CLUS_2              12               185
  CLUS_3              10               154
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               9                87
  CLUS_2              11               107
  CLUS_3               4                60
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              16               143
  CLUS_2              15               132
  CLUS_3              13               128
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              12               120
  CLUS_2              23               188
  CLUS_3               9                95
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              27               170
  CLUS_2              15               164
  CLUS_3               5                92
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2              27               187
  CLUS_3              18               172
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               8                96
  CLUS_2              24               160
  CLUS_3              12               131
  CLUS_4               4                40
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              14               151
  CLUS_2              31               228
  CLUS_3               3                48

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3455        TCGA-AK-3456 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3455        TCGA-AK-3456 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3               129
  CLUS_2               1               196
  CLUS_3               3               161
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                95
  CLUS_2               1               117
  CLUS_3               1                63
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4               155
  CLUS_2               0               147
  CLUS_3               2               139
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               0               211
  CLUS_3               5                99
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               196
  CLUS_2               4               175
  CLUS_3               2                95
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2               1               213
  CLUS_3               4               186
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1               103
  CLUS_2               0               184
  CLUS_3               6               137
  CLUS_4               0                44
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3               162
  CLUS_2               2               257
  CLUS_3               2                49

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                33
  CLUS_2               3                21
  CLUS_3               1                12
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                20
  CLUS_3               0                33
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              16               116
  CLUS_2               2               195
  CLUS_3               9               155
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               9                87
  CLUS_2               3               115
  CLUS_3               3                61
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              16               143
  CLUS_2               4               143
  CLUS_3               6               135
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               8               124
  CLUS_2               5               206
  CLUS_3              13                91
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4               193
  CLUS_2              20               159
  CLUS_3               3                94
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                64
  CLUS_2               5               209
  CLUS_3              17               173
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                99
  CLUS_2               3               181
  CLUS_3              17               126
  CLUS_4               2                42
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              11               154
  CLUS_2               8               251
  CLUS_3               8                43

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4P GAIN WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4P GAIN WILD-TYPE" 
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               128
  CLUS_2               1               196
  CLUS_3               3               161
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                94
  CLUS_2               1               117
  CLUS_3               0                64
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               155
  CLUS_2               0               147
  CLUS_3               2               139
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               1               210
  CLUS_3               4               100
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               197
  CLUS_2               4               175
  CLUS_3               3                94
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2               2               212
  CLUS_3               3               187
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               103
  CLUS_2               0               184
  CLUS_3               6               137
  CLUS_4               1                43
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3               162
  CLUS_2               3               256
  CLUS_3               2                49

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"4Q GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               129
  CLUS_2               2               195
  CLUS_3               3               161
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                95
  CLUS_2               2               116
  CLUS_3               0                64
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               156
  CLUS_2               0               147
  CLUS_3               3               138
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               2               209
  CLUS_3               3               101
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               197
  CLUS_2               3               176
  CLUS_3               4                93
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2               3               211
  CLUS_3               2               188
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               0               184
  CLUS_3               5               138
  CLUS_4               1                43
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               162
  CLUS_2               3               256
  CLUS_3               2                49

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               9                24
  CLUS_2               4                20
  CLUS_3               2                11
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               4                19
  CLUS_3               9                24
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              58                74
  CLUS_2              52               145
  CLUS_3              31               133
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              30                66
  CLUS_2              33                85
  CLUS_3              14                50
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              49               110
  CLUS_2              44               103
  CLUS_3              35               106
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              45                87
  CLUS_2              55               156
  CLUS_3              28                76
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              63               134
  CLUS_2              52               127
  CLUS_3              18                79
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              10                59
  CLUS_2              71               143
  CLUS_3              52               138
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              19                85
  CLUS_2              65               119
  CLUS_3              42               101
  CLUS_4              13                31
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              44               121
  CLUS_2              86               173
  CLUS_3               9                42

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13                20
  CLUS_2               4                20
  CLUS_3               2                11
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               4                19
  CLUS_3              13                20
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              59                73
  CLUS_2              63               134
  CLUS_3              34               130
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              34                62
  CLUS_2              39                79
  CLUS_3              16                48
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              49               110
  CLUS_2              52                95
  CLUS_3              41               100
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              48                84
  CLUS_2              64               147
  CLUS_3              30                74
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              73               124
  CLUS_2              53               126
  CLUS_3              22                75
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              12                57
  CLUS_2              80               134
  CLUS_3              56               134
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              24                80
  CLUS_2              71               113
  CLUS_3              42               101
  CLUS_4              15                29
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              47               118
  CLUS_2              96               163
  CLUS_3               9                42

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6P GAIN WILD-TYPE" 
D11V2, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6P GAIN WILD-TYPE" 
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               2               195
  CLUS_3               3               161
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                95
  CLUS_2               3               115
  CLUS_3               0                64
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3               156
  CLUS_2               0               147
  CLUS_3               3               138
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               130
  CLUS_2               2               209
  CLUS_3               2               102
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               195
  CLUS_2               1               178
  CLUS_3               3                94
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                68
  CLUS_2               4               210
  CLUS_3               1               189
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3               101
  CLUS_2               2               182
  CLUS_3               1               142
  CLUS_4               0                44
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               2               257
  CLUS_3               2                49

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6Q GAIN WILD-TYPE" 
D12V2, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"6Q GAIN WILD-TYPE" 
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               1               196
  CLUS_3               3               161
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                95
  CLUS_2               2               116
  CLUS_3               0                64
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3               156
  CLUS_2               0               147
  CLUS_3               2               139
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2               130
  CLUS_2               1               210
  CLUS_3               2               102
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2               195
  CLUS_2               1               178
  CLUS_3               2                95
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                68
  CLUS_2               3               211
  CLUS_3               1               189
D12V9, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               2               182
  CLUS_3               1               142
  CLUS_4               0                44
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1               164
  CLUS_2               2               257
  CLUS_3               2                49

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               8                25
  CLUS_2               6                18
  CLUS_3               4                 9
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               6                17
  CLUS_3               8                25
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              55                77
  CLUS_2              34               163
  CLUS_3              38               126
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              28                68
  CLUS_2              22                96
  CLUS_3               9                55
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              49               110
  CLUS_2              28               119
  CLUS_3              39               102
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              42                90
  CLUS_2              41               170
  CLUS_3              33                71
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              43               154
  CLUS_2              57               122
  CLUS_3              22                75
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              12                57
  CLUS_2              52               162
  CLUS_3              58               132
D13V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22                82
  CLUS_2              48               136
  CLUS_3              51                92
  CLUS_4               4                40
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              41               124
  CLUS_2              68               191
  CLUS_3              16                35

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               8                25
  CLUS_2               6                18
  CLUS_3               4                 9
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               6                17
  CLUS_3               8                25
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              54                78
  CLUS_2              34               163
  CLUS_3              41               123
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              30                66
  CLUS_2              23                95
  CLUS_3              10                54
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              52               107
  CLUS_2              26               121
  CLUS_3              40               101
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              45                87
  CLUS_2              39               172
  CLUS_3              34                70
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              43               154
  CLUS_2              58               121
  CLUS_3              23                74
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              14                55
  CLUS_2              51               163
  CLUS_3              59               131
D14V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              22                82
  CLUS_2              48               136
  CLUS_3              53                90
  CLUS_4               4                40
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              44               121
  CLUS_2              68               191
  CLUS_3              15                36

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320        TCGA-A3-3322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325        TCGA-A3-3326 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336        TCGA-A3-3343 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349        TCGA-A3-3351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362        TCGA-A3-3363 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374        TCGA-A3-3378 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383        TCGA-AK-3426 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443        TCGA-AK-3444 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455        TCGA-AK-3456 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                68 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3317        TCGA-A3-3319        TCGA-A3-3320        TCGA-A3-3322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3323        TCGA-A3-3324        TCGA-A3-3325        TCGA-A3-3326 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3331        TCGA-A3-3335        TCGA-A3-3336        TCGA-A3-3343 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3346        TCGA-A3-3347        TCGA-A3-3349        TCGA-A3-3351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3352        TCGA-A3-3359        TCGA-A3-3362        TCGA-A3-3363 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3365        TCGA-A3-3372        TCGA-A3-3374        TCGA-A3-3378 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383        TCGA-AK-3426 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443        TCGA-AK-3444 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455        TCGA-AK-3456 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778        TCGA-B2-3923 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099        TCGA-B2-4102 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161        TCGA-BP-4162 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167        TCGA-CJ-4634 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638        TCGA-CJ-4639 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643        TCGA-CJ-4644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10               122
  CLUS_2               0               197
  CLUS_3               4               160
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               7                89
  CLUS_2               2               116
  CLUS_3               1                63
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              11               148
  CLUS_2               0               147
  CLUS_3               1               140
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6               126
  CLUS_2               3               208
  CLUS_3               3               101
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0               197
  CLUS_2              10               169
  CLUS_3               3                94
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                66
  CLUS_2               0               214
  CLUS_3              10               180
D15V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               1               183
  CLUS_3               9               134
  CLUS_4               2                42
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               7               158
  CLUS_2               3               256
  CLUS_3               4                47

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               0                33
  CLUS_2               2                22
  CLUS_3               2                11
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                21
  CLUS_3               0                33
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              19               113
  CLUS_2               1               196
  CLUS_3              14               150
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                82
  CLUS_2               2               116
  CLUS_3               4                60
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              24               135
  CLUS_2               2               145
  CLUS_3               6               135
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              12               120
  CLUS_2               9               202
  CLUS_3              11                93
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1               196
  CLUS_2              25               154
  CLUS_3               5                92
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                66
  CLUS_2               4               210
  CLUS_3              24               166
D16V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               5                99
  CLUS_2               3               181
  CLUS_3              22               121
  CLUS_4               3                41
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              15               150
  CLUS_2              10               249
  CLUS_3               8                43

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9P GAIN WILD-TYPE" 
D17V2, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9P GAIN WILD-TYPE" 
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               4               193
  CLUS_3               3               161
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                96
  CLUS_2               3               115
  CLUS_3               0                64
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0               159
  CLUS_2               4               143
  CLUS_3               2               139
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0               132
  CLUS_2               4               207
  CLUS_3               2               102
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4               193
  CLUS_2               0               179
  CLUS_3               2                95
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2               4               210
  CLUS_3               0               190
D17V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3               101
  CLUS_2               3               181
  CLUS_3               2               141
  CLUS_4               0                44
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0               165
  CLUS_2               6               253
  CLUS_3               2                49

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9Q GAIN WILD-TYPE" 
D18V2, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                69 
       TCGA-A3-3306        TCGA-A3-3307        TCGA-A3-3308        TCGA-A3-3311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3316        TCGA-A3-3317        TCGA-A3-3319 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3320        TCGA-A3-3322        TCGA-A3-3323        TCGA-A3-3324 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3325        TCGA-A3-3326        TCGA-A3-3331        TCGA-A3-3335 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3336        TCGA-A3-3343        TCGA-A3-3346        TCGA-A3-3347 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3351        TCGA-A3-3352        TCGA-A3-3359 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3363        TCGA-A3-3365        TCGA-A3-3372 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-3378        TCGA-A3-3380        TCGA-A3-3382        TCGA-A3-3383 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3426        TCGA-AK-3427        TCGA-AK-3440        TCGA-AK-3443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3444        TCGA-AK-3447        TCGA-AK-3453        TCGA-AK-3455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3456        TCGA-AK-3465        TCGA-AS-3777        TCGA-AS-3778 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-3923        TCGA-B2-3924        TCGA-B2-4098        TCGA-B2-4099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-4102        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-BP-4161 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4164        TCGA-BP-4167 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4634        TCGA-CJ-4636        TCGA-CJ-4637        TCGA-CJ-4638 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4641        TCGA-CJ-4643 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CJ-4644 
"9Q GAIN WILD-TYPE" 
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               2               195
  CLUS_3               5               159
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                94
  CLUS_2               2               116
  CLUS_3               1                63
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               156
  CLUS_2               1               146
  CLUS_3               2               139
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               131
  CLUS_2               1               210
  CLUS_3               4               100
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3               194
  CLUS_2               2               177
  CLUS_3               3                94
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                67
  CLUS_2               3               211
  CLUS_3               3               187
D18V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               102
  CLUS_2               2               182
  CLUS_3               4               139
  CLUS_4               0                44
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               4               255
  CLUS_3               2                49

Clustering(19) Variable = 10p gain mutation analysis
D19V1, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                129
  CLUS_2                1                196
  CLUS_3                2                162
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                2                116
  CLUS_3                1                 63
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                157
  CLUS_2                2                145
  CLUS_3                1                140
D19V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                3                208
  CLUS_3                1                103
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                196
  CLUS_2                4                175
  CLUS_3                1                 96
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 68
  CLUS_2                1                213
  CLUS_3                4                186
D19V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                2                182
  CLUS_3                3                140
  CLUS_4                1                 43
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                164
  CLUS_2                4                255
  CLUS_3                1                 50

Clustering(20) Variable = 10q gain mutation analysis
D20V1, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V2, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                197
  CLUS_3                2                162
D20V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                1                117
  CLUS_3                1                 63
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                158
  CLUS_2                2                145
  CLUS_3                0                141
D20V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                2                209
  CLUS_3                0                104
D20V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                196
  CLUS_2                2                177
  CLUS_3                1                 96
D20V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 68
  CLUS_2                1                213
  CLUS_3                2                188
D20V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                104
  CLUS_2                1                183
  CLUS_3                2                141
  CLUS_4                1                 43
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                164
  CLUS_2                2                257
  CLUS_3                1                 50

Clustering(21) Variable = 11p gain mutation analysis
D21V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                1                 23
  CLUS_3                1                 12
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 22
  CLUS_3                1                 32
D21V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               11                121
  CLUS_2                1                196
  CLUS_3                5                159
D21V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 92
  CLUS_2                5                113
  CLUS_3                1                 63
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                153
  CLUS_2                2                145
  CLUS_3                7                134
D21V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2                7                204
  CLUS_3                4                100
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                193
  CLUS_2                7                172
  CLUS_3                4                 93
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 67
  CLUS_2                4                210
  CLUS_3                9                181
D21V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                101
  CLUS_2                5                179
  CLUS_3                7                136
  CLUS_4                2                 42
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                157
  CLUS_2                7                252
  CLUS_3                2                 49

Clustering(22) Variable = 11q gain mutation analysis
D22V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                1                 23
  CLUS_3                1                 12
D22V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 22
  CLUS_3                1                 32
D22V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               10                122
  CLUS_2                1                196
  CLUS_3                4                160
D22V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 93
  CLUS_2                5                113
  CLUS_3                1                 63
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                154
  CLUS_2                2                145
  CLUS_3                6                135
D22V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                129
  CLUS_2                6                205
  CLUS_3                4                100
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                193
  CLUS_2                5                174
  CLUS_3                4                 93
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 67
  CLUS_2                4                210
  CLUS_3                7                183
D22V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                102
  CLUS_2                5                179
  CLUS_3                6                137
  CLUS_4                2                 42
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                7                158
  CLUS_2                6                253
  CLUS_3                2                 49

Clustering(23) Variable = 12p gain mutation analysis
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                5                 19
  CLUS_3                1                 12
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                5                 18
  CLUS_3                2                 31
D23V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               37                 95
  CLUS_2               13                184
  CLUS_3               28                136
D23V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               29                 67
  CLUS_2               12                106
  CLUS_3               12                 52
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               41                118
  CLUS_2               12                135
  CLUS_3               16                125
D23V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               24                108
  CLUS_2               23                188
  CLUS_3               22                 82
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               15                182
  CLUS_2               45                134
  CLUS_3               12                 85
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 62
  CLUS_2               18                196
  CLUS_3               47                143
D23V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                 96
  CLUS_2               17                167
  CLUS_3               43                100
  CLUS_4               10                 34
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               27                138
  CLUS_2               39                220
  CLUS_3               12                 39

Clustering(24) Variable = 12q gain mutation analysis
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                5                 19
  CLUS_3                1                 12
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                5                 18
  CLUS_3                2                 31
D24V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               37                 95
  CLUS_2               13                184
  CLUS_3               28                136
D24V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               29                 67
  CLUS_2               12                106
  CLUS_3               12                 52
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               41                118
  CLUS_2               12                135
  CLUS_3               16                125
D24V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               25                107
  CLUS_2               23                188
  CLUS_3               21                 83
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               15                182
  CLUS_2               45                134
  CLUS_3               12                 85
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                7                 62
  CLUS_2               18                196
  CLUS_3               47                143
D24V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                8                 96
  CLUS_2               17                167
  CLUS_3               43                100
  CLUS_4               10                 34
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               27                138
  CLUS_2               39                220
  CLUS_3               12                 39

Clustering(25) Variable = 13q gain mutation analysis
D25V1, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                127
  CLUS_2                5                192
  CLUS_3                4                160
D25V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                7                 89
  CLUS_2                6                112
  CLUS_3                0                 64
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                154
  CLUS_2                2                145
  CLUS_3                6                135
D25V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2                8                203
  CLUS_3                1                103
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                194
  CLUS_2                4                175
  CLUS_3                6                 91
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 66
  CLUS_2                5                209
  CLUS_3                5                185
D25V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                 98
  CLUS_2                4                180
  CLUS_3                2                141
  CLUS_4                2                 42
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                7                158
  CLUS_2                6                253
  CLUS_3                1                 50

Clustering(26) Variable = 14q gain mutation analysis
D26V1, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3378         TCGA-A3-3380 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D26V2, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3378         TCGA-A3-3380 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D26V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                197
  CLUS_3                4                160
D26V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                1                117
  CLUS_3                0                 64
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                156
  CLUS_2                0                147
  CLUS_3                1                140
D26V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                132
  CLUS_2                1                210
  CLUS_3                3                101
D26V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                197
  CLUS_2                1                178
  CLUS_3                4                 93
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 67
  CLUS_2                0                214
  CLUS_3                3                187
D26V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                103
  CLUS_2                0                184
  CLUS_3                3                140
  CLUS_4                1                 43
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                163
  CLUS_2                1                258
  CLUS_3                2                 49

Clustering(27) Variable = 15q gain mutation analysis
D27V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 68 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3378         TCGA-A3-3380         TCGA-A3-3382 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3383         TCGA-AK-3426         TCGA-AK-3427 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3443         TCGA-AK-3444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3447         TCGA-AK-3453         TCGA-AK-3455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3456         TCGA-AK-3465         TCGA-AS-3777 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AS-3778         TCGA-B2-3923         TCGA-B2-3924 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B2-4098         TCGA-B2-4099         TCGA-B2-4102 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4148         TCGA-B8-4151 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4154         TCGA-B8-4619         TCGA-B8-4620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4161         TCGA-BP-4162         TCGA-BP-4163 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4164         TCGA-BP-4167         TCGA-CJ-4634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4636         TCGA-CJ-4637         TCGA-CJ-4638 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4639         TCGA-CJ-4640         TCGA-CJ-4641 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4643         TCGA-CJ-4644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 68 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3378         TCGA-A3-3380         TCGA-A3-3382 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A3-3383         TCGA-AK-3426         TCGA-AK-3427 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3440         TCGA-AK-3443         TCGA-AK-3444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3447         TCGA-AK-3453         TCGA-AK-3455 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AK-3456         TCGA-AK-3465         TCGA-AS-3777 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AS-3778         TCGA-B2-3923         TCGA-B2-3924 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B2-4098         TCGA-B2-4099         TCGA-B2-4102 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4148         TCGA-B8-4151 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B8-4154         TCGA-B8-4619         TCGA-B8-4620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4161         TCGA-BP-4162         TCGA-BP-4163 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BP-4164         TCGA-BP-4167         TCGA-CJ-4634 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4636         TCGA-CJ-4637         TCGA-CJ-4638 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4639         TCGA-CJ-4640         TCGA-CJ-4641 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CJ-4643         TCGA-CJ-4644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                126
  CLUS_2                2                195
  CLUS_3                6                158
D27V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                4                114
  CLUS_3                1                 63
D27V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                155
  CLUS_2                3                144
  CLUS_3                4                137
D27V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2                4                207
  CLUS_3                3                101
D27V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                192
  CLUS_2                2                177
  CLUS_3                5                 92
D27V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                 66
  CLUS_2                6                208
  CLUS_3                3                187
D27V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                100
  CLUS_2                6                178
  CLUS_3                3                140
  CLUS_4                1                 43
D27V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                161
  CLUS_2                8                251
  CLUS_3                2                 49

Clustering(28) Variable = 16p gain mutation analysis
D28V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                6                 18
  CLUS_3                1                 12
D28V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                5                 18
  CLUS_3                2                 31
D28V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               24                108
  CLUS_2               22                175
  CLUS_3               19                145
D28V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               10                 86
  CLUS_2               17                101
  CLUS_3                7                 57
D28V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               23                136
  CLUS_2               16                131
  CLUS_3               19                122
D28V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               23                109
  CLUS_2               23                188
  CLUS_3               12                 92
D28V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               24                173
  CLUS_2               28                151
  CLUS_3               13                 84
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               15                 54
  CLUS_2               25                189
  CLUS_3               25                165
D28V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                9                 95
  CLUS_2               26                158
  CLUS_3               24                119
  CLUS_4                6                 38
D28V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               18                147
  CLUS_2               38                221
  CLUS_3                9                 42

Clustering(29) Variable = 16q gain mutation analysis
D29V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                5                 19
  CLUS_3                1                 12
D29V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                 19
  CLUS_3                1                 32
D29V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               21                111
  CLUS_2               18                179
  CLUS_3               19                145
D29V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               10                 86
  CLUS_2               14                104
  CLUS_3                6                 58
D29V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               21                138
  CLUS_2               13                134
  CLUS_3               17                124
D29V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               19                113
  CLUS_2               21                190
  CLUS_3               11                 93
D29V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               22                175
  CLUS_2               25                154
  CLUS_3               11                 86
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               12                 57
  CLUS_2               23                191
  CLUS_3               23                167
D29V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                9                 95
  CLUS_2               21                163
  CLUS_3               22                121
  CLUS_4                6                 38
D29V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               18                147
  CLUS_2               32                227
  CLUS_3                8                 43

Clustering(30) Variable = 17p gain mutation analysis
D30V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                0                 24
  CLUS_3                3                 10
D30V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                0                 23
  CLUS_3                0                 33
D30V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                126
  CLUS_2                0                197
  CLUS_3               10                154
D30V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                5                113
  CLUS_3                4                 60
D30V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                7                152
  CLUS_2                4                143
  CLUS_3                3                138
D30V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2                4                207
  CLUS_3                6                 98
D30V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                192
  CLUS_2                4                175
  CLUS_3                6                 91
D30V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                 63
  CLUS_2                4                210
  CLUS_3                5                185
D30V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                101
  CLUS_2                4                180
  CLUS_3                8                135
  CLUS_4                1                 43
D30V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                161
  CLUS_2                7                252
  CLUS_3                5                 46

Clustering(31) Variable = 17q gain mutation analysis
D31V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                1                 23
  CLUS_3                3                 10
D31V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                 22
  CLUS_3                0                 33
D31V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                124
  CLUS_2                2                195
  CLUS_3               12                152
D31V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                5                113
  CLUS_3                6                 58
D31V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                150
  CLUS_2                4                143
  CLUS_3                7                134
D31V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                126
  CLUS_2                8                203
  CLUS_3                6                 98
D31V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                191
  CLUS_2                8                171
  CLUS_3                7                 90
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                 61
  CLUS_2                5                209
  CLUS_3                8                182
D31V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                 98
  CLUS_2                5                179
  CLUS_3               10                133
  CLUS_4                1                 43
D31V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                8                157
  CLUS_2                7                252
  CLUS_3                7                 44

Clustering(32) Variable = 18p gain mutation analysis
D32V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                3                 21
  CLUS_3                0                 13
D32V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 20
  CLUS_3                0                 33
D32V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                8                124
  CLUS_2                6                191
  CLUS_3                4                160
D32V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                7                111
  CLUS_3                2                 62
D32V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                156
  CLUS_2                7                140
  CLUS_3                6                135
D32V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2               11                200
  CLUS_3                1                103
D32V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                193
  CLUS_2                6                173
  CLUS_3                7                 90
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 65
  CLUS_2                8                206
  CLUS_3                5                185
D32V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                100
  CLUS_2                6                178
  CLUS_3                4                139
  CLUS_4                4                 40
D32V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                6                159
  CLUS_2                9                250
  CLUS_3                3                 48

Clustering(33) Variable = 18q gain mutation analysis
D33V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                3                 21
  CLUS_3                0                 13
D33V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 20
  CLUS_3                0                 33
D33V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                8                124
  CLUS_2                6                191
  CLUS_3                4                160
D33V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                7                111
  CLUS_3                2                 62
D33V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                156
  CLUS_2                7                140
  CLUS_3                6                135
D33V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2               11                200
  CLUS_3                1                103
D33V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                193
  CLUS_2                6                173
  CLUS_3                7                 90
D33V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 65
  CLUS_2                8                206
  CLUS_3                5                185
D33V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                100
  CLUS_2                6                178
  CLUS_3                4                139
  CLUS_4                4                 40
D33V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                6                159
  CLUS_2                9                250
  CLUS_3                3                 48

Clustering(34) Variable = 19p gain mutation analysis
D34V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                2                 22
  CLUS_3                1                 12
D34V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 21
  CLUS_3                0                 33
D34V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               14                118
  CLUS_2                1                196
  CLUS_3               10                154
D34V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 88
  CLUS_2                5                113
  CLUS_3                2                 62
D34V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               13                146
  CLUS_2                4                143
  CLUS_3                6                135
D34V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                7                125
  CLUS_2                8                203
  CLUS_3                8                 96
D34V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                193
  CLUS_2               12                167
  CLUS_3                7                 90
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                 65
  CLUS_2                4                210
  CLUS_3               15                175
D34V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                101
  CLUS_2                5                179
  CLUS_3               13                130
  CLUS_4                4                 40
D34V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                9                156
  CLUS_2               10                249
  CLUS_3                6                 45

Clustering(35) Variable = 19q gain mutation analysis
D35V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                2                 22
  CLUS_3                2                 11
D35V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 21
  CLUS_3                0                 33
D35V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               17                115
  CLUS_2                1                196
  CLUS_3               10                154
D35V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                9                 87
  CLUS_2                5                113
  CLUS_3                2                 62
D35V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               15                144
  CLUS_2                4                143
  CLUS_3                7                134
D35V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                8                124
  CLUS_2                8                203
  CLUS_3               10                 94
D35V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                193
  CLUS_2               14                165
  CLUS_3                7                 90
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 65
  CLUS_2                4                210
  CLUS_3               17                173
D35V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                101
  CLUS_2                5                179
  CLUS_3               15                128
  CLUS_4                4                 40
D35V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                155
  CLUS_2               10                249
  CLUS_3                7                 44

Clustering(36) Variable = 20p gain mutation analysis
D36V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                3                 21
  CLUS_3                3                 10
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                3                 20
  CLUS_3                1                 32
D36V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               36                 96
  CLUS_2                3                194
  CLUS_3               27                137
D36V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               24                 72
  CLUS_2                8                110
  CLUS_3                7                 57
D36V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               36                123
  CLUS_2                8                139
  CLUS_3               17                124
D36V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               16                116
  CLUS_2               21                190
  CLUS_3               24                 80
D36V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               12                185
  CLUS_2               42                137
  CLUS_3               10                 87
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                8                 61
  CLUS_2               13                201
  CLUS_3               43                147
D36V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                8                 96
  CLUS_2               13                171
  CLUS_3               37                106
  CLUS_4                8                 36
D36V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               27                138
  CLUS_2               26                233
  CLUS_3               13                 38

Clustering(37) Variable = 20q gain mutation analysis
D37V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                4                 20
  CLUS_3                3                 10
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                4                 19
  CLUS_3                1                 32
D37V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               39                 93
  CLUS_2                3                194
  CLUS_3               26                138
D37V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               24                 72
  CLUS_2                8                110
  CLUS_3                7                 57
D37V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               37                122
  CLUS_2                8                139
  CLUS_3               18                123
D37V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               18                114
  CLUS_2               21                190
  CLUS_3               24                 80
D37V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               12                185
  CLUS_2               45                134
  CLUS_3                9                 88
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                 61
  CLUS_2               13                201
  CLUS_3               45                145
D37V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                7                 97
  CLUS_2               13                171
  CLUS_3               40                103
  CLUS_4                8                 36
D37V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               27                138
  CLUS_2               27                232
  CLUS_3               14                 37

Clustering(38) Variable = 21q gain mutation analysis
D38V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                2                 22
  CLUS_3                0                 13
D38V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 21
  CLUS_3                2                 31
D38V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               20                112
  CLUS_2                6                191
  CLUS_3                7                157
D38V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               11                 85
  CLUS_2                5                113
  CLUS_3                3                 61
D38V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               13                146
  CLUS_2                9                138
  CLUS_3                8                133
D38V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               11                121
  CLUS_2               13                198
  CLUS_3                6                 98
D38V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                8                189
  CLUS_2               18                161
  CLUS_3                6                 91
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 66
  CLUS_2               10                204
  CLUS_3               19                171
D38V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 99
  CLUS_2               11                173
  CLUS_3               15                128
  CLUS_4                2                 42
D38V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               12                153
  CLUS_2               18                241
  CLUS_3                3                 48

Clustering(39) Variable = 22q gain mutation analysis
D39V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                2                 22
  CLUS_3                0                 13
D39V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 20
  CLUS_3                0                 33
D39V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               15                117
  CLUS_2                3                194
  CLUS_3                7                157
D39V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                 89
  CLUS_2                7                111
  CLUS_3                0                 64
D39V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                151
  CLUS_2                6                141
  CLUS_3                9                132
D39V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                128
  CLUS_2               15                196
  CLUS_3                4                100
D39V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                9                188
  CLUS_2                9                170
  CLUS_3                6                 91
D39V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                 66
  CLUS_2               10                204
  CLUS_3               11                179
D39V9, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                 98
  CLUS_2                8                176
  CLUS_3                7                136
  CLUS_4                3                 41
D39V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               10                155
  CLUS_2               11                248
  CLUS_3                3                 48

Clustering(40) Variable = Xq gain mutation analysis
D40V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                31
  CLUS_2               0                24
  CLUS_3               1                12
D40V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                23
  CLUS_3               2                31
D40V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4               128
  CLUS_2               3               194
  CLUS_3               4               160
D40V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                95
  CLUS_2               4               114
  CLUS_3               1                63
D40V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               156
  CLUS_2               3               144
  CLUS_3               2               139
D40V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               129
  CLUS_2               3               208
  CLUS_3               2               102
D40V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2               195
  CLUS_2               4               175
  CLUS_3               4                93
D40V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                66
  CLUS_2               3               211
  CLUS_3               4               186
D40V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0               104
  CLUS_2               4               180
  CLUS_3               6               137
  CLUS_4               1                43
D40V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2               163
  CLUS_2               6               253
  CLUS_3               3                48

Clustering(41) Variable = 1p loss mutation analysis
D41V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                31
  CLUS_2               2                22
  CLUS_3               7                 6
D41V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               8                 6
  CLUS_2               1                22
  CLUS_3               2                31
D41V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               9               123
  CLUS_2               5               192
  CLUS_3              18               146
D41V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                94
  CLUS_2               6               112
  CLUS_3               5                59
D41V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              10               149
  CLUS_2               6               141
  CLUS_3              10               131
D41V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3               129
  CLUS_2              10               201
  CLUS_3              13                91
D41V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               9               188
  CLUS_2               8               171
  CLUS_3              13                84
D41V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              15                54
  CLUS_2               9               205
  CLUS_3               6               184
D41V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               7                97
  CLUS_2               7               177
  CLUS_3              18               125
  CLUS_4               0                44
D41V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6               159
  CLUS_2              10               249
  CLUS_3              16                35

Clustering(42) Variable = 1q loss mutation analysis
D42V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                31
  CLUS_2               2                22
  CLUS_3               5                 8
D42V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               1                22
  CLUS_3               2                31
D42V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               130
  CLUS_2               2               195
  CLUS_3              17               147
D42V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                94
  CLUS_2               4               114
  CLUS_3               2                62
D42V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6               153
  CLUS_2               4               143
  CLUS_3               7               134
D42V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               130
  CLUS_2               6               205
  CLUS_3               9                95
D42V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               5               192
  CLUS_2               3               176
  CLUS_3              13                84
D42V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              13                56
  CLUS_2               5               209
  CLUS_3               3               187
D42V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3               101
  CLUS_2               5               179
  CLUS_3              13               130
  CLUS_4               0                44
D42V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2               163
  CLUS_2               6               253
  CLUS_3              13                38

Clustering(43) Variable = 2p loss mutation analysis
D43V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                33
  CLUS_2               1                23
  CLUS_3               5                 8
D43V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               1                22
  CLUS_3               0                33
D43V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               197
  CLUS_3              10               154
D43V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                96
  CLUS_2               2               116
  CLUS_3               1                63
D43V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               156
  CLUS_2               0               147
  CLUS_3               3               138
D43V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               211
  CLUS_3               6                98
D43V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               197
  CLUS_2               0               179
  CLUS_3               9                88
D43V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9                60
  CLUS_2               0               214
  CLUS_3               0               190
D43V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1               103
  CLUS_2               0               184
  CLUS_3               9               134
  CLUS_4               0                44
D43V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               165
  CLUS_2               0               259
  CLUS_3              10                41

Clustering(44) Variable = 2q loss mutation analysis
D44V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                33
  CLUS_2               1                23
  CLUS_3               5                 8
D44V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               1                22
  CLUS_3               0                33
D44V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               197
  CLUS_3              11               153
D44V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                95
  CLUS_2               2               116
  CLUS_3               1                63
D44V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               4               155
  CLUS_2               0               147
  CLUS_3               3               138
D44V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               132
  CLUS_2               0               211
  CLUS_3               7                97
D44V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               197
  CLUS_2               0               179
  CLUS_3              10                87
D44V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9                60
  CLUS_2               0               214
  CLUS_3               1               189
D44V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               103
  CLUS_2               0               184
  CLUS_3              10               133
  CLUS_4               0                44
D44V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               165
  CLUS_2               1               258
  CLUS_3              10                41

Clustering(45) Variable = 3p loss mutation analysis
D45V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              21                12
  CLUS_2              12                12
  CLUS_3               2                11
D45V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2              13                10
  CLUS_3              20                13
D45V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1             107                25
  CLUS_2             148                49
  CLUS_3              49               115
D45V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              61                35
  CLUS_2              88                30
  CLUS_3              29                35
D45V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              82                77
  CLUS_2             114                33
  CLUS_3              81                60
D45V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              86                46
  CLUS_2             146                65
  CLUS_3              45                59
D45V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1             154                43
  CLUS_2              95                84
  CLUS_3              39                58
D45V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              23                46
  CLUS_2             160                54
  CLUS_3             105                85
D45V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              55                49
  CLUS_2             136                48
  CLUS_3              69                74
  CLUS_4              31                13
D45V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              83                82
  CLUS_2             188                71
  CLUS_3              20                31

Clustering(46) Variable = 3q loss mutation analysis
D46V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                28
  CLUS_2               2                22
  CLUS_3               1                12
D46V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                21
  CLUS_3               5                28
D46V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              30               102
  CLUS_2              30               167
  CLUS_3              13               151
D46V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              17                79
  CLUS_2              19                99
  CLUS_3               5                59
D46V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              19               140
  CLUS_2              28               119
  CLUS_3              22               119
D46V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              23               109
  CLUS_2              40               171
  CLUS_3               6                98
D46V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              25               172
  CLUS_2              25               154
  CLUS_3              17                80
D46V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              10                59
  CLUS_2              28               186
  CLUS_3              29               161
D46V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              10                94
  CLUS_2              27               157
  CLUS_3              20               123
  CLUS_4              14                30
D46V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              26               139
  CLUS_2              41               218
  CLUS_3               4                47

Clustering(47) Variable = 4p loss mutation analysis
D47V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                30
  CLUS_2               0                24
  CLUS_3               0                13
D47V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                23
  CLUS_3               3                30
D47V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              15               117
  CLUS_2               9               188
  CLUS_3              11               153
D47V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              12                84
  CLUS_2               8               110
  CLUS_3               4                60
D47V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              14               145
  CLUS_2              12               135
  CLUS_3               8               133
D47V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9               123
  CLUS_2              17               194
  CLUS_3               8                96
D47V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              16               181
  CLUS_2              14               165
  CLUS_3               2                95
D47V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                67
  CLUS_2              17               197
  CLUS_3              13               177
D47V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               8                96
  CLUS_2              17               167
  CLUS_3               8               135
  CLUS_4               1                43
D47V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              13               152
  CLUS_2              19               240
  CLUS_3               2                49

Clustering(48) Variable = 4q loss mutation analysis
D48V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                31
  CLUS_2               1                23
  CLUS_3               0                13
D48V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                22
  CLUS_3               2                31
D48V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              16               116
  CLUS_2               3               194
  CLUS_3               9               155
D48V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              10                86
  CLUS_2               6               112
  CLUS_3               3                61
D48V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11               148
  CLUS_2               8               139
  CLUS_3               9               132
D48V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5               127
  CLUS_2              14               197
  CLUS_3               9                95
D48V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11               186
  CLUS_2              13               166
  CLUS_3               1                96
D48V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                69
  CLUS_2              12               202
  CLUS_3              13               177
D48V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               6                98
  CLUS_2              13               171
  CLUS_3               8               135
  CLUS_4               1                43
D48V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11               154
  CLUS_2              16               243
  CLUS_3               1                50

Clustering(49) Variable = 6p loss mutation analysis
D49V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                31
  CLUS_2               6                18
  CLUS_3               5                 8
D49V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               7                16
  CLUS_3               1                32
D49V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              37                95
  CLUS_2               4               193
  CLUS_3              17               147
D49V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              17                79
  CLUS_2               6               112
  CLUS_3               5                59
D49V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              37               122
  CLUS_2               4               143
  CLUS_3              11               130
D49V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              17               115
  CLUS_2              10               201
  CLUS_3              25                79
D49V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              11               186
  CLUS_2              32               147
  CLUS_3              10                87
D49V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               9                60
  CLUS_2              12               202
  CLUS_3              32               158
D49V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               101
  CLUS_2              13               171
  CLUS_3              38               105
  CLUS_4               2                42
D49V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              16               149
  CLUS_2              24               235
  CLUS_3              16                35

Clustering(50) Variable = 6q loss mutation analysis
D50V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               4                29
  CLUS_2               7                17
  CLUS_3               6                 7
D50V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               8                15
  CLUS_3               3                30
D50V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              54                78
  CLUS_2               9               188
  CLUS_3              19               145
D50V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              20                76
  CLUS_2              14               104
  CLUS_3               7                57
D50V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              46               113
  CLUS_2              17               130
  CLUS_3              12               129
D50V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              25               107
  CLUS_2              22               189
  CLUS_3              28                76
D50V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              29               168
  CLUS_2              36               143
  CLUS_3              12                85
D50V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12                57
  CLUS_2              30               184
  CLUS_3              35               155
D50V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8                96
  CLUS_2              27               157
  CLUS_3              42               101
  CLUS_4               3                41
D50V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              19               146
  CLUS_2              42               217
  CLUS_3              19                32

Clustering(51) Variable = 8p loss mutation analysis
D51V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                28
  CLUS_2               5                19
  CLUS_3               3                10
D51V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               5                18
  CLUS_3               5                28
D51V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              34                98
  CLUS_2              29               168
  CLUS_3              31               133
D51V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              19                77
  CLUS_2              19                99
  CLUS_3              13                51
D51V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              32               127
  CLUS_2              29               118
  CLUS_3              24               117
D51V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              26               106
  CLUS_2              37               174
  CLUS_3              22                82
D51V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              41               156
  CLUS_2              36               143
  CLUS_3              12                85
D51V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              10                59
  CLUS_2              41               173
  CLUS_3              38               152
D51V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              21                83
  CLUS_2              31               153
  CLUS_3              36               107
  CLUS_4               6                38
D51V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              35               130
  CLUS_2              49               210
  CLUS_3              10                41

Clustering(52) Variable = 8q loss mutation analysis
D52V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                31
  CLUS_2               1                23
  CLUS_3               2                11
D52V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                22
  CLUS_3               2                31
D52V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               8               124
  CLUS_2              15               182
  CLUS_3              14               150
D52V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               7                89
  CLUS_2              12               106
  CLUS_3               2                62
D52V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              10               149
  CLUS_2              14               133
  CLUS_3              10               131
D52V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               8               124
  CLUS_2              19               192
  CLUS_3               7                97
D52V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              21               176
  CLUS_2               9               170
  CLUS_3               6                91
D52V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                65
  CLUS_2              24               190
  CLUS_3               8               182
D52V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              12                92
  CLUS_2              14               170
  CLUS_3              10               133
  CLUS_4               1                43
D52V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              14               151
  CLUS_2              19               240
  CLUS_3               4                47

Clustering(53) Variable = 9p loss mutation analysis
D53V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                29
  CLUS_2               6                18
  CLUS_3               1                12
D53V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               7                16
  CLUS_3               3                30
D53V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              60                72
  CLUS_2               3               194
  CLUS_3              24               140
D53V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              38                58
  CLUS_2               3               115
  CLUS_3              10                54
D53V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              44               115
  CLUS_2              17               130
  CLUS_3              21               120
D53V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              28               104
  CLUS_2              30               181
  CLUS_3              24                80
D53V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              14               183
  CLUS_2              60               119
  CLUS_3               9                88
D53V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                64
  CLUS_2              15               199
  CLUS_3              63               127
D53V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                93
  CLUS_2              16               168
  CLUS_3              50                93
  CLUS_4               8                36
D53V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              36               129
  CLUS_2              38               221
  CLUS_3              11                40

Clustering(54) Variable = 9q loss mutation analysis
D54V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                29
  CLUS_2               6                18
  CLUS_3               1                12
D54V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               7                16
  CLUS_3               3                30
D54V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              64                68
  CLUS_2               4               193
  CLUS_3              24               140
D54V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              40                56
  CLUS_2               3               115
  CLUS_3              10                54
D54V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              46               113
  CLUS_2              18               129
  CLUS_3              23               118
D54V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              31               101
  CLUS_2              30               181
  CLUS_3              26                78
D54V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              15               182
  CLUS_2              64               115
  CLUS_3               9                88
D54V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                64
  CLUS_2              15               199
  CLUS_3              68               122
D54V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              11                93
  CLUS_2              16               168
  CLUS_3              53                90
  CLUS_4               9                35
D54V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              38               127
  CLUS_2              40               219
  CLUS_3              11                40

Clustering(55) Variable = 10p loss mutation analysis
D55V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                2                 22
  CLUS_3                4                  9
D55V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                2                 21
  CLUS_3                1                 32
D55V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                122
  CLUS_2                3                194
  CLUS_3               19                145
D55V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                 86
  CLUS_2                7                111
  CLUS_3                3                 61
D55V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               12                147
  CLUS_2                6                141
  CLUS_3                9                132
D55V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                128
  CLUS_2               12                199
  CLUS_3               11                 93
D55V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                9                188
  CLUS_2                8                171
  CLUS_3               13                 84
D55V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                 59
  CLUS_2               10                204
  CLUS_3               10                180
D55V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                8                 96
  CLUS_2                9                175
  CLUS_3               12                131
  CLUS_4                3                 41
D55V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                155
  CLUS_2               13                246
  CLUS_3                9                 42

Clustering(56) Variable = 10q loss mutation analysis
D56V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                2                 22
  CLUS_3                4                  9
D56V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                2                 21
  CLUS_3                2                 31
D56V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               20                112
  CLUS_2                9                188
  CLUS_3               19                145
D56V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               16                 80
  CLUS_2               10                108
  CLUS_3                3                 61
D56V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               17                142
  CLUS_2               11                136
  CLUS_3               15                126
D56V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                126
  CLUS_2               21                190
  CLUS_3               16                 88
D56V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               15                182
  CLUS_2               15                164
  CLUS_3               15                 82
D56V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               11                 58
  CLUS_2               16                198
  CLUS_3               18                172
D56V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                 96
  CLUS_2               16                168
  CLUS_3               17                126
  CLUS_4                7                 37
D56V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               16                149
  CLUS_2               23                236
  CLUS_3                9                 42

Clustering(57) Variable = 11p loss mutation analysis
D57V1, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D57V2, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D57V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                197
  CLUS_3                3                161
D57V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                1                117
  CLUS_3                0                 64
D57V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                156
  CLUS_2                1                146
  CLUS_3                0                141
D57V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                132
  CLUS_2                1                210
  CLUS_3                3                101
D57V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                196
  CLUS_2                2                177
  CLUS_3                2                 95
D57V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 68
  CLUS_2                1                213
  CLUS_3                3                187
D57V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                1                183
  CLUS_3                3                140
  CLUS_4                0                 44
D57V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                2                257
  CLUS_3                1                 50

Clustering(58) Variable = 11q loss mutation analysis
D58V1, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D58V2, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D58V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                129
  CLUS_2                0                197
  CLUS_3                4                160
D58V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                1                117
  CLUS_3                1                 63
D58V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                156
  CLUS_2                2                145
  CLUS_3                0                141
D58V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                132
  CLUS_2                2                209
  CLUS_3                3                101
D58V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                196
  CLUS_2                3                176
  CLUS_3                2                 95
D58V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 68
  CLUS_2                1                213
  CLUS_3                4                186
D58V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                102
  CLUS_2                1                183
  CLUS_3                4                139
  CLUS_4                0                 44
D58V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                161
  CLUS_2                2                257
  CLUS_3                1                 50

Clustering(59) Variable = 13q loss mutation analysis
D59V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                4                 20
  CLUS_3                2                 11
D59V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                 19
  CLUS_3                0                 33
D59V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               14                118
  CLUS_2                2                195
  CLUS_3               15                149
D59V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                8                 88
  CLUS_2                4                114
  CLUS_3                5                 59
D59V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               17                142
  CLUS_2                2                145
  CLUS_3                9                132
D59V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                123
  CLUS_2                6                205
  CLUS_3               13                 91
D59V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                193
  CLUS_2               17                162
  CLUS_3                9                 88
D59V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 62
  CLUS_2                4                210
  CLUS_3               19                171
D59V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 97
  CLUS_2                3                181
  CLUS_3               20                123
  CLUS_4                1                 43
D59V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               13                152
  CLUS_2                9                250
  CLUS_3                9                 42

Clustering(60) Variable = 14q loss mutation analysis
D60V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                7                 26
  CLUS_2               15                  9
  CLUS_3                2                 11
D60V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2               15                  8
  CLUS_3                6                 27
D60V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               73                 59
  CLUS_2               41                156
  CLUS_3               44                120
D60V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               43                 53
  CLUS_2               20                 98
  CLUS_3               23                 41
D60V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               77                 82
  CLUS_2               40                107
  CLUS_3               32                109
D60V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               62                 70
  CLUS_2               50                161
  CLUS_3               37                 67
D60V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               54                143
  CLUS_2               88                 91
  CLUS_3               11                 86
D60V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 61
  CLUS_2               60                154
  CLUS_3               85                105
D60V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               27                 77
  CLUS_2               51                133
  CLUS_3               70                 73
  CLUS_4                6                 38
D60V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               40                125
  CLUS_2               89                170
  CLUS_3               25                 26

Clustering(61) Variable = 15q loss mutation analysis
D61V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                2                 22
  CLUS_3                0                 13
D61V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 21
  CLUS_3                1                 32
D61V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                7                125
  CLUS_2                1                196
  CLUS_3                4                160
D61V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 93
  CLUS_2                2                116
  CLUS_3                0                 64
D61V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                153
  CLUS_2                2                145
  CLUS_3                4                137
D61V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                128
  CLUS_2                4                207
  CLUS_3                4                100
D61V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                193
  CLUS_2                8                171
  CLUS_3                0                 97
D61V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 69
  CLUS_2                4                210
  CLUS_3                8                182
D61V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                4                180
  CLUS_3                7                136
  CLUS_4                0                 44
D61V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                161
  CLUS_2                5                254
  CLUS_3                3                 48

Clustering(62) Variable = 16q loss mutation analysis
D62V1, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3307         TCGA-A3-3308         TCGA-A3-3311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3313         TCGA-A3-3316         TCGA-A3-3317 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3319         TCGA-A3-3320         TCGA-A3-3322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D62V2, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3307         TCGA-A3-3308         TCGA-A3-3311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3313         TCGA-A3-3316         TCGA-A3-3317 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3319         TCGA-A3-3320         TCGA-A3-3322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D62V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                128
  CLUS_2                0                197
  CLUS_3                1                163
D62V4, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                276 
        TCGA-A3-3357         TCGA-A3-3358         TCGA-A3-3367 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3370         TCGA-A3-3373         TCGA-A3-3376 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A3-3385         TCGA-A3-3387         TCGA-AK-3425 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3428         TCGA-AK-3431         TCGA-AK-3433 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3434         TCGA-AK-3440         TCGA-AK-3445 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3450         TCGA-AK-3453         TCGA-AK-3454 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3458         TCGA-AK-3460         TCGA-AK-3461 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4688         TCGA-B0-4690         TCGA-B0-4691 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4693         TCGA-B0-4694         TCGA-B0-4696 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4697         TCGA-B0-4698         TCGA-B0-4699 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4700         TCGA-B0-4701         TCGA-B0-4703 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4706         TCGA-B0-4707         TCGA-B0-4710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4712         TCGA-B0-4713         TCGA-B0-4714 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4718         TCGA-B0-4810         TCGA-B0-4811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4813         TCGA-B0-4814         TCGA-B0-4815 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4816         TCGA-B0-4817         TCGA-B0-4818 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4819         TCGA-B0-4821         TCGA-B0-4822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4823         TCGA-B0-4824         TCGA-B0-4827 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4828         TCGA-B0-4841         TCGA-B0-4842 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4843         TCGA-B0-4844         TCGA-B0-4845 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4846         TCGA-B0-4847         TCGA-B0-4848 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-4849         TCGA-B0-4852         TCGA-B0-4945 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5080         TCGA-B0-5092         TCGA-B0-5094 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5095         TCGA-B0-5096         TCGA-B0-5097 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5098         TCGA-B0-5099         TCGA-B0-5100 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5102         TCGA-B0-5104         TCGA-B0-5106 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5107         TCGA-B0-5108         TCGA-B0-5109 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5110         TCGA-B0-5113         TCGA-B0-5115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5116         TCGA-B0-5117         TCGA-B0-5119 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5120         TCGA-B0-5121         TCGA-B0-5399 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5400         TCGA-B0-5690         TCGA-B0-5691 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5692         TCGA-B0-5693         TCGA-B0-5694 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5696         TCGA-B0-5697 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5698         TCGA-B0-5699         TCGA-B0-5701 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5702         TCGA-B0-5703         TCGA-B0-5705 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5706         TCGA-B0-5709         TCGA-B0-5710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5711         TCGA-B0-5712         TCGA-B0-5713 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B0-5812         TCGA-B2-4101         TCGA-B2-5633 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-5635         TCGA-B2-5639         TCGA-B2-5641 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4146         TCGA-B8-4153         TCGA-B8-4621 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-B8-5159 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-5162         TCGA-B8-5163         TCGA-B8-5164 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-5165         TCGA-B8-5545         TCGA-B8-5546 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B8-5552         TCGA-B8-5553         TCGA-BP-4177 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-4760         TCGA-BP-4782         TCGA-BP-4795 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-4801         TCGA-BP-4993         TCGA-BP-5010 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5168         TCGA-BP-5169         TCGA-BP-5170 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5173         TCGA-BP-5174         TCGA-BP-5175 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5176         TCGA-BP-5177         TCGA-BP-5178 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5180         TCGA-BP-5181         TCGA-BP-5182 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5183         TCGA-BP-5184         TCGA-BP-5185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5186         TCGA-BP-5187         TCGA-BP-5189 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5190         TCGA-BP-5191         TCGA-BP-5192 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5194         TCGA-BP-5195         TCGA-BP-5196 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5198         TCGA-BP-5199         TCGA-BP-5200 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BP-5201         TCGA-BP-5202         TCGA-CJ-4869 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4882         TCGA-CJ-4897         TCGA-CJ-4901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4902         TCGA-CJ-4903         TCGA-CJ-4904 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4905         TCGA-CJ-4907         TCGA-CJ-4908 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4912         TCGA-CJ-4913         TCGA-CJ-4916 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-4918         TCGA-CJ-4920         TCGA-CJ-4923 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-5671         TCGA-CJ-5672         TCGA-CJ-5675 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-5676         TCGA-CJ-5677         TCGA-CJ-5678 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-5679         TCGA-CJ-5680         TCGA-CJ-5681 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-5682         TCGA-CJ-5683         TCGA-CJ-5684 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-5686         TCGA-CJ-5689         TCGA-CJ-6027 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CJ-6030         TCGA-CJ-6031 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CJ-6032         TCGA-CJ-6033         TCGA-CW-5580 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CW-5581         TCGA-CW-5583         TCGA-CW-5584 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CW-5585         TCGA-CW-5587         TCGA-CW-5588 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CW-5589         TCGA-CW-5591         TCGA-CW-6087 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CW-6088         TCGA-CW-6090         TCGA-CW-6093 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CW-6097         TCGA-CZ-4853         TCGA-CZ-4856 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4859         TCGA-CZ-4863         TCGA-CZ-4864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4865         TCGA-CZ-4866         TCGA-CZ-5451 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5452         TCGA-CZ-5453         TCGA-CZ-5454 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5455         TCGA-CZ-5456         TCGA-CZ-5457 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5459         TCGA-CZ-5460 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5461         TCGA-CZ-5462         TCGA-CZ-5463 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5464         TCGA-CZ-5465         TCGA-CZ-5466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5467         TCGA-CZ-5468         TCGA-CZ-5469 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5470         TCGA-CZ-5982         TCGA-CZ-5984 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5985         TCGA-CZ-5986         TCGA-CZ-5987 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5988         TCGA-CZ-5989         TCGA-DV-5565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D62V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                157
  CLUS_2                1                146
  CLUS_3                2                139
D62V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                2                209
  CLUS_3                1                103
D62V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                195
  CLUS_2                2                177
  CLUS_3                1                 96
D62V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 69
  CLUS_2                1                213
  CLUS_3                4                186
D62V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                1                183
  CLUS_3                1                142
  CLUS_4                1                 43
D62V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                162
  CLUS_2                1                258
  CLUS_3                0                 51

Clustering(63) Variable = 17p loss mutation analysis
D63V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                3                 21
  CLUS_3                6                  7
D63V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                  8
  CLUS_2                3                 20
  CLUS_3                0                 33
D63V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               12                120
  CLUS_2                0                197
  CLUS_3               13                151
D63V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 92
  CLUS_2                3                115
  CLUS_3                2                 62
D63V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                148
  CLUS_2                1                146
  CLUS_3                9                132
D63V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                128
  CLUS_2                3                208
  CLUS_3               14                 90
D63V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                197
  CLUS_2               12                167
  CLUS_3               11                 86
D63V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               12                 57
  CLUS_2                0                214
  CLUS_3               11                179
D63V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                101
  CLUS_2                0                184
  CLUS_3               21                122
  CLUS_4                1                 43
D63V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                9                156
  CLUS_2                3                256
  CLUS_3               13                 38

Clustering(64) Variable = 17q loss mutation analysis
D64V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                2                 22
  CLUS_3                5                  8
D64V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                2                 21
  CLUS_3                0                 33
D64V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                197
  CLUS_3               10                154
D64V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 96
  CLUS_2                2                116
  CLUS_3                1                 63
D64V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                155
  CLUS_2                0                147
  CLUS_3                4                137
D64V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                132
  CLUS_2                0                211
  CLUS_3                8                 96
D64V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                197
  CLUS_2                1                178
  CLUS_3                9                 88
D64V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                9                 60
  CLUS_2                0                214
  CLUS_3                1                189
D64V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                0                184
  CLUS_3               11                132
  CLUS_4                0                 44
D64V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                165
  CLUS_2                1                258
  CLUS_3               11                 40

Clustering(65) Variable = 18p loss mutation analysis
D65V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                5                 19
  CLUS_3                1                 12
D65V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                 19
  CLUS_3                2                 31
D65V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               26                106
  CLUS_2                6                191
  CLUS_3               14                150
D65V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                 84
  CLUS_2                4                114
  CLUS_3                8                 56
D65V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               28                131
  CLUS_2                3                144
  CLUS_3               11                130
D65V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               17                115
  CLUS_2               11                200
  CLUS_3               14                 90
D65V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                8                189
  CLUS_2               32                147
  CLUS_3                4                 93
D65V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                 62
  CLUS_2                8                206
  CLUS_3               29                161
D65V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                9                 95
  CLUS_2                6                178
  CLUS_3               29                114
  CLUS_4                2                 42
D65V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               17                148
  CLUS_2               18                241
  CLUS_3               11                 40

Clustering(66) Variable = 18q loss mutation analysis
D66V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 31
  CLUS_2                5                 19
  CLUS_3                2                 11
D66V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                4                 19
  CLUS_3                2                 31
D66V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               27                105
  CLUS_2                7                190
  CLUS_3               14                150
D66V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               13                 83
  CLUS_2                5                113
  CLUS_3                8                 56
D66V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               29                130
  CLUS_2                4                143
  CLUS_3               12                129
D66V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               17                115
  CLUS_2               14                197
  CLUS_3               14                 90
D66V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                188
  CLUS_2               32                147
  CLUS_3                5                 92
D66V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                 60
  CLUS_2                9                205
  CLUS_3               28                162
D66V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               10                 94
  CLUS_2                7                177
  CLUS_3               29                114
  CLUS_4                2                 42
D66V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               16                149
  CLUS_2               19                240
  CLUS_3               13                 38

Clustering(67) Variable = 19p loss mutation analysis
D67V1, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3465         TCGA-AS-3777         TCGA-AS-3778 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-3923         TCGA-B2-3924         TCGA-B2-4098 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-4099         TCGA-B2-4102         TCGA-B8-4143 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4148         TCGA-B8-4151         TCGA-B8-4154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4619         TCGA-B8-4620         TCGA-BP-4161 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4162         TCGA-BP-4163         TCGA-BP-4167 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D67V2, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3319         TCGA-A3-3320 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3322         TCGA-A3-3323         TCGA-A3-3324 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3325         TCGA-A3-3326         TCGA-A3-3331 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3336         TCGA-A3-3343 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3346         TCGA-A3-3347         TCGA-A3-3349 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3359 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3365 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3372         TCGA-A3-3374         TCGA-A3-3378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3382         TCGA-A3-3383 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3427         TCGA-AK-3440 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3444         TCGA-AK-3447 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3453         TCGA-AK-3455         TCGA-AK-3456 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3465         TCGA-AS-3777         TCGA-AS-3778 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-3923         TCGA-B2-3924         TCGA-B2-4098 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-4099         TCGA-B2-4102         TCGA-B8-4143 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4148         TCGA-B8-4151         TCGA-B8-4154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B8-4619         TCGA-B8-4620         TCGA-BP-4161 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BP-4162         TCGA-BP-4163         TCGA-BP-4167 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D67V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                0                197
  CLUS_3                2                162
D67V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                0                118
  CLUS_3                1                 63
D67V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                155
  CLUS_2                0                147
  CLUS_3                0                141
D67V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                131
  CLUS_2                0                211
  CLUS_3                3                101
D67V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                196
  CLUS_2                1                178
  CLUS_3                2                 95
D67V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 69
  CLUS_2                1                213
  CLUS_3                3                187
D67V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                1                183
  CLUS_3                2                141
  CLUS_4                0                 44
D67V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                2                257
  CLUS_3                0                 51

Clustering(68) Variable = 20p loss mutation analysis
D68V1, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3320         TCGA-A3-3322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D68V2, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 69 
        TCGA-A3-3306         TCGA-A3-3307         TCGA-A3-3308 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3311         TCGA-A3-3313         TCGA-A3-3316 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3320         TCGA-A3-3322 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3323         TCGA-A3-3324         TCGA-A3-3325 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3326         TCGA-A3-3331         TCGA-A3-3335 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3336         TCGA-A3-3343         TCGA-A3-3346 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3359         TCGA-A3-3362 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3363         TCGA-A3-3365         TCGA-A3-3372 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3378         TCGA-A3-3380 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-3382         TCGA-A3-3383         TCGA-AK-3426 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3440         TCGA-AK-3443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3444         TCGA-AK-3447         TCGA-AK-3453 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3455         TCGA-AK-3456         TCGA-AK-3465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AS-3777         TCGA-AS-3778         TCGA-B2-3923 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-3924         TCGA-B2-4098         TCGA-B2-4099 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-4102         TCGA-B8-4143         TCGA-B8-4148 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4620         TCGA-BP-4161         TCGA-BP-4162 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4164         TCGA-BP-4167 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4634         TCGA-CJ-4636         TCGA-CJ-4637 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CJ-4641         TCGA-CJ-4643         TCGA-CJ-4644 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D68V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                128
  CLUS_2                2                195
  CLUS_3                0                164
D68V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 95
  CLUS_2                1                117
  CLUS_3                1                 63
D68V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                156
  CLUS_2                1                146
  CLUS_3                2                139
D68V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                130
  CLUS_2                2                209
  CLUS_3                2                102
D68V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                196
  CLUS_2                4                175
  CLUS_3                1                 96
D68V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 68
  CLUS_2                2                212
  CLUS_3                3                187
D68V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                102
  CLUS_2                0                184
  CLUS_3                4                139
  CLUS_4                0                 44
D68V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                163
  CLUS_2                2                257
  CLUS_3                2                 49

Clustering(69) Variable = 21q loss mutation analysis
D69V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                1                 23
  CLUS_3                4                  9
D69V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                 22
  CLUS_3                1                 32
D69V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                6                126
  CLUS_2                5                192
  CLUS_3               21                143
D69V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                 88
  CLUS_2                6                112
  CLUS_3                6                 58
D69V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               10                149
  CLUS_2                9                138
  CLUS_3                7                134
D69V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                6                126
  CLUS_2                8                203
  CLUS_3               12                 92
D69V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                189
  CLUS_2                7                172
  CLUS_3               14                 83
D69V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               14                 55
  CLUS_2                6                208
  CLUS_3                9                181
D69V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                7                 97
  CLUS_2                9                175
  CLUS_3               16                127
  CLUS_4                0                 44
D69V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                8                157
  CLUS_2               13                246
  CLUS_3               11                 40

Clustering(70) Variable = 22q loss mutation analysis
D70V1, multiclass
D70V2, multiclass
D70V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                126
  CLUS_2                0                197
  CLUS_3                5                159
D70V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 91
  CLUS_2                1                117
  CLUS_3                1                 63
D70V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                7                152
  CLUS_2                3                144
  CLUS_3                1                140
D70V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                126
  CLUS_2                3                208
  CLUS_3                2                102
D70V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                196
  CLUS_2               10                169
  CLUS_3                0                 97
D70V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 69
  CLUS_2                2                212
  CLUS_3                9                181
D70V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                103
  CLUS_2                4                180
  CLUS_3                6                137
  CLUS_4                0                 44
D70V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                160
  CLUS_2                5                254
  CLUS_3                1                 50

Clustering(71) Variable = Xq loss mutation analysis
D71V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                33
  CLUS_2               1                23
  CLUS_3               2                11
D71V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                22
  CLUS_3               0                33
D71V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2               130
  CLUS_2               1               196
  CLUS_3               4               160
D71V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                94
  CLUS_2               1               117
  CLUS_3               1                63
D71V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               158
  CLUS_2               1               146
  CLUS_3               2               139
D71V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               131
  CLUS_2               1               210
  CLUS_3               2               102
D71V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               196
  CLUS_2               2               177
  CLUS_3               4                93
D71V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                66
  CLUS_2               0               214
  CLUS_3               4               186
D71V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               104
  CLUS_2               1               183
  CLUS_3               6               137
  CLUS_4               0                44
D71V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               164
  CLUS_2               2               257
  CLUS_3               4                47
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"             "RPPA_CNMF"    "RPPA_CHIERARCHICAL" 
                     V7                      V8                      V9 
         "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF" 
                    V10 
 "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
