
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/334384/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/COAD-TP/2662550/1.GDAC_mergedClustering.Finished/COAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=COAD-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=COAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=425, in cluster file=413, common to both=413
[1] "Reduce the number of clustering variables from 80 to 76."
[1]  76 413
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               402 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               402 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               366 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               366 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               373 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               40               373 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               39               374 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               39               374 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20               393 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20               393 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30               383 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               30               383 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               410 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3               410 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               408 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               408 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               39               374 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               39               374 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               21               392 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               21               392 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               50               363 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               50               363 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               45               368 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               45               368 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              200               213 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              200               213 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              175               238 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              175               238 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               80               333 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               80               333 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              162               251 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              162               251 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               46               367 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               46               367 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               39               374 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               39               374 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                18                395 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                18                395 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                406 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                406 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                395 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                18                395 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                22                391 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                22                391 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                66                347 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                66                347 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                60                353 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                60                353 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               211                202 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               211                202 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                398 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                15                398 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                408 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                408 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                67                346 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                67                346 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                66                347 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                66                347 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                404 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                404 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                48                365 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                48                365 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                398 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                398 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                404 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                404 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                34                379 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                34                379 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                41                372 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                41                372 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               188                225 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               188                225 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               267                146 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               267                146 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                402 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                402 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               401 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               12               401 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               362 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               362 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18               395 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18               395 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               409 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               409 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               407 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               407 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               27               386 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               27               386 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               401 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               401 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               84               329 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               84               329 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               68               345 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               68               345 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               388 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               388 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38               375 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               38               375 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               401 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               401 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21               392 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21               392 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               93               320 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               93               320 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8               405 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8               405 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               27               386 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               27               386 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               26               387 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               26               387 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                391 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                391 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                389 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                389 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                22                391 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                22                391 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                27                386 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                27                386 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                392 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                392 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                393 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                393 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                407 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                407 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                94                319 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                94                319 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                99                314 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                99                314 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                404 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                404 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                406 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                406 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               164                249 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               164                249 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                381 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                381 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               209                204 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               209                204 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               225                188 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               225                188 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                399 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                399 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                400 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                400 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                33                380 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                33                380 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                71                342 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                71                342 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                81                332 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                81                332 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               408 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               408 
[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 413 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	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 413 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2               146 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A6-3810        TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3673        TCGA-AA-3675        TCGA-AA-3678        TCGA-AA-3680 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3966        TCGA-AA-3968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3977        TCGA-AA-3979        TCGA-AA-3982 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01C        TCGA-AA-A01D        TCGA-AA-A01F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02E        TCGA-AA-A02F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02R        TCGA-AA-A02W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071 
"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               146 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A6-3810        TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3673        TCGA-AA-3675        TCGA-AA-3678        TCGA-AA-3680 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3966        TCGA-AA-3968 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3977        TCGA-AA-3979        TCGA-AA-3982 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01C        TCGA-AA-A01D        TCGA-AA-A01F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02E        TCGA-AA-A02F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02R        TCGA-AA-A02W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               6               164
  CLUS_2               4               183
  CLUS_3               0                32
  CLUS_4               1                23
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               102
  CLUS_2               4                82
  CLUS_3               2                61
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               2               115
  CLUS_3               1                 6
  CLUS_4               0                76
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3               139
  CLUS_2               0                23
  CLUS_3               0                48
  CLUS_4               3                48
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                65
  CLUS_2               1                57
  CLUS_3               1                38
  CLUS_4               0                20
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               2                16
  CLUS_3               1               101
D1V9, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5               169
  CLUS_2               3               160
  CLUS_3               3                58
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5               167
  CLUS_2               1                43
  CLUS_3               5               177

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8                55
  CLUS_2               0                32
  CLUS_3               3                27
  CLUS_4               0                23
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                42
  CLUS_2               5                43
  CLUS_3               0                13
  CLUS_4               4                39
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              23               147
  CLUS_2              14               173
  CLUS_3               6                26
  CLUS_4               4                20
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              17                88
  CLUS_2              11                75
  CLUS_3               5                58
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9                55
  CLUS_2              14               103
  CLUS_3               1                 6
  CLUS_4               6                70
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              16               126
  CLUS_2               3                20
  CLUS_3               2                46
  CLUS_4               9                42
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              11                56
  CLUS_2               4                54
  CLUS_3               2                37
  CLUS_4               0                20
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                58
  CLUS_2               2                16
  CLUS_3               9                93
D2V9, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              18               156
  CLUS_2              19               144
  CLUS_3              10                51
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              19               153
  CLUS_2               6                38
  CLUS_3              22               160

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               8                55
  CLUS_2               0                32
  CLUS_3               1                29
  CLUS_4               2                21
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                44
  CLUS_2               4                44
  CLUS_3               1                12
  CLUS_4               6                37
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              27               143
  CLUS_2               9               178
  CLUS_3               2                30
  CLUS_4               2                22
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              17                88
  CLUS_2               7                79
  CLUS_3               3                60
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               6                58
  CLUS_2              18                99
  CLUS_3               0                 7
  CLUS_4               4                72
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              17               125
  CLUS_2               1                22
  CLUS_3               3                45
  CLUS_4               7                44
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              10                57
  CLUS_2               0                58
  CLUS_3               2                37
  CLUS_4               2                18
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               1                17
  CLUS_3              13                89
D3V9, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              14               160
  CLUS_2              19               144
  CLUS_3               6                55
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              13               159
  CLUS_2               4                40
  CLUS_3              22               160

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               9                54
  CLUS_2               0                32
  CLUS_3               1                29
  CLUS_4               2                21
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                44
  CLUS_2               5                43
  CLUS_3               1                12
  CLUS_4               6                37
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              28               142
  CLUS_2               6               181
  CLUS_3               3                29
  CLUS_4               2                22
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              18                87
  CLUS_2               6                80
  CLUS_3               1                62
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5                59
  CLUS_2              18                99
  CLUS_3               0                 7
  CLUS_4               4                72
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              17               125
  CLUS_2               1                22
  CLUS_3               3                45
  CLUS_4               6                45
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              11                56
  CLUS_2               0                58
  CLUS_3               2                37
  CLUS_4               2                18
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                64
  CLUS_2               1                17
  CLUS_3              14                88
D4V9, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              14               160
  CLUS_2              19               144
  CLUS_3               5                56
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              13               159
  CLUS_2               4                40
  CLUS_3              21               161

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                59
  CLUS_2               0                32
  CLUS_3               1                29
  CLUS_4               2                21
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               2                46
  CLUS_3               0                13
  CLUS_4               4                39
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              13               157
  CLUS_2               4               183
  CLUS_3               2                30
  CLUS_4               1                23
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               7                98
  CLUS_2               5                81
  CLUS_3               1                62
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               7               110
  CLUS_3               0                 7
  CLUS_4               2                74
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              10               132
  CLUS_2               0                23
  CLUS_3               0                48
  CLUS_4               2                49
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                63
  CLUS_2               2                56
  CLUS_3               0                39
  CLUS_4               1                19
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                18
  CLUS_3               5                97
D5V9, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               7               167
  CLUS_2              10               153
  CLUS_3               2                59
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               7               165
  CLUS_2               0                44
  CLUS_3              12               170

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                58
  CLUS_2               1                31
  CLUS_3               1                29
  CLUS_4               3                20
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               2                46
  CLUS_3               0                13
  CLUS_4               7                36
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              20               150
  CLUS_2               4               183
  CLUS_3               3                29
  CLUS_4               3                21
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              11                94
  CLUS_2               7                79
  CLUS_3               2                61
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                59
  CLUS_2              10               107
  CLUS_3               1                 6
  CLUS_4               3                73
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              13               129
  CLUS_2               1                22
  CLUS_3               1                47
  CLUS_4               4                47
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                61
  CLUS_2               3                55
  CLUS_3               0                39
  CLUS_4               2                18
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               0                18
  CLUS_3               8                94
D6V9, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              12               162
  CLUS_2              15               148
  CLUS_3               2                59
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              11               161
  CLUS_2               3                41
  CLUS_3              15               167

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
D7V2, multiclass
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2               168
  CLUS_2               1               186
  CLUS_3               0                32
  CLUS_4               0                24
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2               103
  CLUS_2               0                86
  CLUS_3               1                62
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               0               117
  CLUS_3               0                 7
  CLUS_4               2                74
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               141
  CLUS_2               0                23
  CLUS_3               2                46
  CLUS_4               0                51
D7V7, multiclass
D7V8, multiclass
D7V9, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               174
  CLUS_2               2               161
  CLUS_3               1                60
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               172
  CLUS_2               2                42
  CLUS_3               1               181

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               146 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-3810        TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3675        TCGA-AA-3678 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3695 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3841        TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3864        TCGA-AA-3866 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3966        TCGA-AA-3968 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3977        TCGA-AA-3979        TCGA-AA-3982 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01C        TCGA-AA-A01D        TCGA-AA-A01F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02E        TCGA-AA-A02F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02R        TCGA-AA-A02W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               146 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-3810        TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3675        TCGA-AA-3678 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3695 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3841        TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3864        TCGA-AA-3866 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3966        TCGA-AA-3968 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3977        TCGA-AA-3979        TCGA-AA-3982 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01C        TCGA-AA-A01D        TCGA-AA-A01F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02E        TCGA-AA-A02F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02R        TCGA-AA-A02W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               167
  CLUS_2               2               185
  CLUS_3               0                32
  CLUS_4               0                24
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               104
  CLUS_2               1                85
  CLUS_3               1                62
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1               116
  CLUS_3               0                 7
  CLUS_4               1                75
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2               140
  CLUS_2               0                23
  CLUS_3               1                47
  CLUS_4               0                51
D8V7, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               182 
       TCGA-A6-2670        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2679 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-3807        TCGA-A6-3810 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-4107        TCGA-AA-3488        TCGA-AA-3492        TCGA-AA-3494 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3495        TCGA-AA-3502        TCGA-AA-3506        TCGA-AA-3514 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3524 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3525        TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3531        TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3542        TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3688 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841        TCGA-AA-3842 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3860 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3870 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3966        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3982        TCGA-AA-3984        TCGA-AA-3986 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A02E        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02R        TCGA-AA-A02W        TCGA-AA-A03F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071        TCGA-AZ-4308 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AZ-4313        TCGA-AZ-4315        TCGA-AZ-4614        TCGA-AZ-4615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4684        TCGA-CA-5256        TCGA-CK-4951 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V8, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               182 
       TCGA-A6-2670        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2679 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-3807        TCGA-A6-3810 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A6-4107        TCGA-AA-3488        TCGA-AA-3492        TCGA-AA-3494 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3495        TCGA-AA-3502        TCGA-AA-3506        TCGA-AA-3514 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3524 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3525        TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3531        TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3542        TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3688 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841        TCGA-AA-3842 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3860 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3869        TCGA-AA-3870 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3966        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3982        TCGA-AA-3984        TCGA-AA-3986 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A02E        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02R        TCGA-AA-A02W        TCGA-AA-A03F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071        TCGA-AZ-4308 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AZ-4313        TCGA-AZ-4315        TCGA-AZ-4614        TCGA-AZ-4615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4684        TCGA-CA-5256        TCGA-CK-4951 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               171
  CLUS_2               1               162
  CLUS_3               1                60
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3               169
  CLUS_2               1                43
  CLUS_3               1               181

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8                55
  CLUS_2               1                31
  CLUS_3               2                28
  CLUS_4               4                19
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               4                44
  CLUS_3               2                11
  CLUS_4               8                35
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              19               151
  CLUS_2               9               178
  CLUS_3               8                24
  CLUS_4               3                21
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               6                99
  CLUS_2              14                72
  CLUS_3               3                60
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                60
  CLUS_2              14               103
  CLUS_3               1                 6
  CLUS_4               7                69
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              15               127
  CLUS_2               2                21
  CLUS_3               4                44
  CLUS_4               5                46
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               9                58
  CLUS_2               3                55
  CLUS_3               5                34
  CLUS_4               3                17
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                60
  CLUS_2               2                16
  CLUS_3              14                88
D9V9, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              19               155
  CLUS_2              16               147
  CLUS_3               4                57
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              20               152
  CLUS_2               4                40
  CLUS_3              15               167

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                61
  CLUS_2               1                31
  CLUS_3               2                28
  CLUS_4               2                21
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                43
  CLUS_2               2                46
  CLUS_3               2                11
  CLUS_4               2                41
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               157
  CLUS_2               4               183
  CLUS_3               3                29
  CLUS_4               1                23
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5               100
  CLUS_2               7                79
  CLUS_3               1                62
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                63
  CLUS_2               9               108
  CLUS_3               0                 7
  CLUS_4               4                72
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              11               131
  CLUS_2               0                23
  CLUS_3               2                46
  CLUS_4               1                50
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               4                63
  CLUS_2               3                55
  CLUS_3               2                37
  CLUS_4               1                19
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               2                16
  CLUS_3               5                97
D10V9, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               9               165
  CLUS_2               9               154
  CLUS_3               3                58
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              10               162
  CLUS_2               2                42
  CLUS_3               9               173

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              11                52
  CLUS_2               6                26
  CLUS_3               2                28
  CLUS_4               3                20
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               5                39
  CLUS_2               4                44
  CLUS_3               0                13
  CLUS_4              13                30
D11V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              30               140
  CLUS_2              15               172
  CLUS_3               4                28
  CLUS_4               1                23
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              13                92
  CLUS_2               8                78
  CLUS_3               5                58
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              10                54
  CLUS_2              14               103
  CLUS_3               1                 6
  CLUS_4               7                69
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              19               123
  CLUS_2               2                21
  CLUS_3               5                43
  CLUS_4               6                45
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              10                57
  CLUS_2               9                49
  CLUS_3               2                37
  CLUS_4               4                16
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               7                57
  CLUS_2               3                15
  CLUS_3              15                87
D11V9, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              24               150
  CLUS_2              18               145
  CLUS_3               5                56
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              24               148
  CLUS_2               2                42
  CLUS_3              21               161

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              10                53
  CLUS_2               5                27
  CLUS_3               1                29
  CLUS_4               3                20
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                39
  CLUS_2               3                45
  CLUS_3               0                13
  CLUS_4              11                32
D12V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              28               142
  CLUS_2              14               173
  CLUS_3               2                30
  CLUS_4               1                23
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              12                93
  CLUS_2               9                77
  CLUS_3               3                60
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               7                57
  CLUS_2              13               104
  CLUS_3               1                 6
  CLUS_4               7                69
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              16               126
  CLUS_2               1                22
  CLUS_3               5                43
  CLUS_4               6                45
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              10                57
  CLUS_2               7                51
  CLUS_3               2                37
  CLUS_4               3                17
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               7                57
  CLUS_2               2                16
  CLUS_3              13                89
D12V9, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              22               152
  CLUS_2              17               146
  CLUS_3               4                57
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              22               150
  CLUS_2               2                42
  CLUS_3              19               163

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              38                25
  CLUS_2               7                25
  CLUS_3               9                21
  CLUS_4               9                14
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              10                34
  CLUS_2              22                26
  CLUS_3               4                 9
  CLUS_4              27                16
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1             112                58
  CLUS_2              49               138
  CLUS_3              23                 9
  CLUS_4              16                 8
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              71                34
  CLUS_2              38                48
  CLUS_3              23                40
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              33                31
  CLUS_2              61                56
  CLUS_3               4                 3
  CLUS_4              30                46
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              73                69
  CLUS_2               7                16
  CLUS_3              17                31
  CLUS_4              31                20
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              48                19
  CLUS_2              18                40
  CLUS_3              10                29
  CLUS_4              10                10
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              16                48
  CLUS_2              11                 7
  CLUS_3              59                43
D13V9, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              82                92
  CLUS_2              86                77
  CLUS_3              27                34
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              83                89
  CLUS_2              22                22
  CLUS_3              90                92

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              32                31
  CLUS_2               5                27
  CLUS_3               8                22
  CLUS_4               9                14
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               9                35
  CLUS_2              18                30
  CLUS_3               4                 9
  CLUS_4              23                20
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              96                74
  CLUS_2              45               142
  CLUS_3              21                11
  CLUS_4              13                11
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              61                44
  CLUS_2              34                52
  CLUS_3              21                42
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28                36
  CLUS_2              49                68
  CLUS_3               4                 3
  CLUS_4              28                48
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              59                83
  CLUS_2               7                16
  CLUS_3              15                33
  CLUS_4              28                23
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              40                27
  CLUS_2              16                42
  CLUS_3               9                30
  CLUS_4              10                10
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              14                50
  CLUS_2              10                 8
  CLUS_3              51                51
D14V9, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              72               102
  CLUS_2              75                88
  CLUS_3              23                38
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              72               100
  CLUS_2              17                27
  CLUS_3              81               101

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              11                52
  CLUS_2               6                26
  CLUS_3               5                25
  CLUS_4               4                19
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                36
  CLUS_2               9                39
  CLUS_3               2                11
  CLUS_4               7                36
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              23               147
  CLUS_2              32               155
  CLUS_3              12                20
  CLUS_4              13                11
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              23                82
  CLUS_2              23                63
  CLUS_3               7                56
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              13                51
  CLUS_2              25                92
  CLUS_3               2                 5
  CLUS_4               9                67
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              28               114
  CLUS_2               6                17
  CLUS_3               4                44
  CLUS_4              11                40
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              15                52
  CLUS_2               7                51
  CLUS_3               8                31
  CLUS_4               3                17
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10                54
  CLUS_2               3                15
  CLUS_3              20                82
D15V9, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              35               139
  CLUS_2              34               129
  CLUS_3               9                52
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              34               138
  CLUS_2              11                33
  CLUS_3              33               149

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              24                39
  CLUS_2              10                22
  CLUS_3              10                20
  CLUS_4              10                13
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              13                31
  CLUS_2              19                29
  CLUS_3               2                11
  CLUS_4              20                23
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              78                92
  CLUS_2              45               142
  CLUS_3              17                15
  CLUS_4              22                 2
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              58                47
  CLUS_2              29                57
  CLUS_3              18                45
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              29                35
  CLUS_2              44                73
  CLUS_3               3                 4
  CLUS_4              27                49
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              53                89
  CLUS_2               8                15
  CLUS_3              14                34
  CLUS_4              28                23
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              30                37
  CLUS_2              16                42
  CLUS_3              14                25
  CLUS_4              10                10
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              18                46
  CLUS_2               8                10
  CLUS_3              44                58
D16V9, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              68               106
  CLUS_2              71                92
  CLUS_3              17                44
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              67               105
  CLUS_2              23                21
  CLUS_3              66               116

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               8                55
  CLUS_2               0                32
  CLUS_3               5                25
  CLUS_4               5                18
D17V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                40
  CLUS_2               8                40
  CLUS_3               3                10
  CLUS_4               3                40
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              21               149
  CLUS_2              16               171
  CLUS_3               6                26
  CLUS_4               3                21
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              12                93
  CLUS_2              11                75
  CLUS_3               4                59
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6                58
  CLUS_2              10               107
  CLUS_3               3                 4
  CLUS_4               7                69
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              14               128
  CLUS_2               5                18
  CLUS_3               5                43
  CLUS_4               2                49
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               7                60
  CLUS_2               3                55
  CLUS_3               6                33
  CLUS_4               5                15
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               8                56
  CLUS_2               0                18
  CLUS_3              13                89
D17V9, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              21               153
  CLUS_2              18               145
  CLUS_3               5                56
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              21               151
  CLUS_2               5                39
  CLUS_3              18               164

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7                56
  CLUS_2               0                32
  CLUS_3               5                25
  CLUS_4               4                19
D18V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                41
  CLUS_2               8                40
  CLUS_3               2                11
  CLUS_4               3                40
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              16               154
  CLUS_2              13               174
  CLUS_3               7                25
  CLUS_4               3                21
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               9                96
  CLUS_2              11                75
  CLUS_3               2                61
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                62
  CLUS_2               8               109
  CLUS_3               3                 4
  CLUS_4               5                71
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              11               131
  CLUS_2               4                19
  CLUS_3               3                45
  CLUS_4               0                51
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6                61
  CLUS_2               4                54
  CLUS_3               5                34
  CLUS_4               3                17
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7                57
  CLUS_2               1                17
  CLUS_3              10                92
D18V9, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              17               157
  CLUS_2              18               145
  CLUS_3               1                60
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              17               155
  CLUS_2               5                39
  CLUS_3              14               168

Clustering(19) Variable = 10p gain mutation analysis
D19V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                 60
  CLUS_2                2                 30
  CLUS_3                0                 30
  CLUS_4                1                 22
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 42
  CLUS_2                1                 47
  CLUS_3                1                 12
  CLUS_4                2                 41
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               10                160
  CLUS_2                4                183
  CLUS_3                2                 30
  CLUS_4                2                 22
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                5                100
  CLUS_2                7                 79
  CLUS_3                0                 63
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                5                112
  CLUS_3                0                  7
  CLUS_4                4                 72
D19V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                6                136
  CLUS_2                0                 23
  CLUS_3                3                 45
  CLUS_4                3                 48
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 65
  CLUS_2                3                 55
  CLUS_3                1                 38
  CLUS_4                0                 20
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 17
  CLUS_3                4                 98
D19V9, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                7                167
  CLUS_2                9                154
  CLUS_3                2                 59
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                7                165
  CLUS_2                2                 42
  CLUS_3                9                173

Clustering(20) Variable = 10q gain mutation analysis
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                3                167
  CLUS_2                2                185
  CLUS_3                0                 32
  CLUS_4                2                 22
D20V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                104
  CLUS_2                5                 81
  CLUS_3                0                 63
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                115
  CLUS_3                0                  7
  CLUS_4                2                 74
D20V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                140
  CLUS_2                0                 23
  CLUS_3                2                 46
  CLUS_4                1                 50
D20V7, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                183 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3812 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3814         TCGA-AA-3818         TCGA-AA-3819 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3841         TCGA-AA-3842 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3845         TCGA-AA-3846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3979         TCGA-AA-3982 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01C         TCGA-AA-A01D         TCGA-AA-A01F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02O 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A02R         TCGA-AA-A02W         TCGA-AA-A03F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AY-4070         TCGA-AY-4071 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AZ-4308         TCGA-AZ-4313         TCGA-AZ-4315 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AZ-4614         TCGA-AZ-4615         TCGA-AZ-4681 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AZ-4684         TCGA-CA-5256         TCGA-CK-4951 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4748 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CM-4750         TCGA-CM-4752         TCGA-CM-5341 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V8, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                183 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3812 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3814         TCGA-AA-3818         TCGA-AA-3819 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3841         TCGA-AA-3842 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3845         TCGA-AA-3846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3979         TCGA-AA-3982 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01C         TCGA-AA-A01D         TCGA-AA-A01F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02O 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A02R         TCGA-AA-A02W         TCGA-AA-A03F 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AY-4070         TCGA-AY-4071 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AZ-4308         TCGA-AZ-4313         TCGA-AZ-4315 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AZ-4614         TCGA-AZ-4615         TCGA-AZ-4681 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AZ-4684         TCGA-CA-5256         TCGA-CK-4951 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4748 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CM-4750         TCGA-CM-4752         TCGA-CM-5341 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V9, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                173
  CLUS_2                5                158
  CLUS_3                1                 60
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                171
  CLUS_2                0                 44
  CLUS_3                6                176

Clustering(21) Variable = 11p gain mutation analysis
D21V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 59
  CLUS_2                0                 32
  CLUS_3                0                 30
  CLUS_4                2                 21
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                0                 48
  CLUS_3                0                 13
  CLUS_4                6                 37
D21V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               16                154
  CLUS_2                1                186
  CLUS_3                1                 31
  CLUS_4                0                 24
D21V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               11                 94
  CLUS_2                0                 86
  CLUS_3                1                 62
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                4                113
  CLUS_3                0                  7
  CLUS_4                3                 73
D21V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                138
  CLUS_2                1                 22
  CLUS_3                1                 47
  CLUS_4                3                 48
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                0                 58
  CLUS_3                0                 39
  CLUS_4                2                 18
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 17
  CLUS_3                8                 94
D21V9, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                9                165
  CLUS_2                7                156
  CLUS_3                1                 60
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                164
  CLUS_2                2                 42
  CLUS_3                7                175

Clustering(22) Variable = 11q gain mutation analysis
D22V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                7                 56
  CLUS_2                0                 32
  CLUS_3                0                 30
  CLUS_4                3                 20
D22V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                2                 46
  CLUS_3                0                 13
  CLUS_4                8                 35
D22V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               19                151
  CLUS_2                0                187
  CLUS_3                2                 30
  CLUS_4                1                 23
D22V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               11                 94
  CLUS_2                1                 85
  CLUS_3                0                 63
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                7                110
  CLUS_3                1                  6
  CLUS_4                2                 74
D22V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                134
  CLUS_2                0                 23
  CLUS_3                1                 47
  CLUS_4                3                 48
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                9                 58
  CLUS_2                0                 58
  CLUS_3                0                 39
  CLUS_4                3                 17
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                1                 17
  CLUS_3               11                 91
D22V9, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               11                163
  CLUS_2                9                154
  CLUS_3                1                 60
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               11                161
  CLUS_2                2                 42
  CLUS_3                8                174

Clustering(23) Variable = 12p gain mutation analysis
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                 55
  CLUS_2                7                 25
  CLUS_3                8                 22
  CLUS_4                4                 19
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 37
  CLUS_2                7                 41
  CLUS_3                6                  7
  CLUS_4                7                 36
D23V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               16                154
  CLUS_2               36                151
  CLUS_3                6                 26
  CLUS_4                8                 16
D23V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                 94
  CLUS_2               20                 66
  CLUS_3                5                 58
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                8                 56
  CLUS_2               16                101
  CLUS_3                2                  5
  CLUS_4               13                 63
D23V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               24                118
  CLUS_2                2                 21
  CLUS_3                8                 40
  CLUS_4                5                 46
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               10                 57
  CLUS_2                9                 49
  CLUS_3               11                 28
  CLUS_4                1                 19
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                 55
  CLUS_2                2                 16
  CLUS_3               20                 82
D23V9, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               32                142
  CLUS_2               28                135
  CLUS_3                4                 57
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               32                140
  CLUS_2                9                 35
  CLUS_3               23                159

Clustering(24) Variable = 12q gain mutation analysis
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                7                 56
  CLUS_2                7                 25
  CLUS_3                8                 22
  CLUS_4                4                 19
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                8                 36
  CLUS_2                8                 40
  CLUS_3                5                  8
  CLUS_4                5                 38
D24V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               13                157
  CLUS_2               36                151
  CLUS_3                4                 28
  CLUS_4                7                 17
D24V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                 96
  CLUS_2               19                 67
  CLUS_3                3                 60
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                7                 57
  CLUS_2               14                103
  CLUS_3                2                  5
  CLUS_4               12                 64
D24V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               22                120
  CLUS_2                2                 21
  CLUS_3                7                 41
  CLUS_4                4                 47
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                 58
  CLUS_2               10                 48
  CLUS_3               10                 29
  CLUS_4                1                 19
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               10                 54
  CLUS_2                2                 16
  CLUS_3               18                 84
D24V9, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               30                144
  CLUS_2               26                137
  CLUS_3                2                 59
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               30                142
  CLUS_2                7                 37
  CLUS_3               21                161

Clustering(25) Variable = 13q gain mutation analysis
D25V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               46                 17
  CLUS_2               10                 22
  CLUS_3                8                 22
  CLUS_4               14                  9
D25V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               11                 33
  CLUS_2               30                 18
  CLUS_3                6                  7
  CLUS_4               31                 12
D25V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1              143                 27
  CLUS_2               42                145
  CLUS_3               11                 21
  CLUS_4               15                  9
D25V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               70                 35
  CLUS_2               35                 51
  CLUS_3               26                 37
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               32                 32
  CLUS_2               71                 46
  CLUS_3                3                  4
  CLUS_4               33                 43
D25V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               83                 59
  CLUS_2               11                 12
  CLUS_3               16                 32
  CLUS_4               29                 22
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               49                 18
  CLUS_2               18                 40
  CLUS_3               12                 27
  CLUS_4               13                  7
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               17                 47
  CLUS_2                9                  9
  CLUS_3               66                 36
D25V9, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               89                 85
  CLUS_2               92                 71
  CLUS_3               23                 38
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               89                 83
  CLUS_2               26                 18
  CLUS_3               89                 93

Clustering(26) Variable = 14q gain mutation analysis
D26V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 62
  CLUS_2                2                 30
  CLUS_3                2                 28
  CLUS_4                1                 22
D26V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                 41
  CLUS_2                1                 47
  CLUS_3                1                 12
  CLUS_4                1                 42
D26V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                6                164
  CLUS_2                4                183
  CLUS_3                2                 30
  CLUS_4                3                 21
D26V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                101
  CLUS_2                4                 82
  CLUS_3                0                 63
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                116
  CLUS_3                1                  6
  CLUS_4                4                 72
D26V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                139
  CLUS_2                0                 23
  CLUS_3                3                 45
  CLUS_4                1                 50
D26V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 66
  CLUS_2                3                 55
  CLUS_3                3                 36
  CLUS_4                0                 20
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                0                 18
  CLUS_3                3                 99
D26V9, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                7                167
  CLUS_2                6                157
  CLUS_3                2                 59
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                7                165
  CLUS_2                2                 42
  CLUS_3                6                176

Clustering(27) Variable = 15q gain mutation analysis
D27V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                147 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3538         TCGA-AA-3542 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3543         TCGA-AA-3544         TCGA-AA-3548 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3552         TCGA-AA-3553 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3555         TCGA-AA-3556 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3560         TCGA-AA-3561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3664         TCGA-AA-3666 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3675         TCGA-AA-3678         TCGA-AA-3679 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3715         TCGA-AA-3811 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3841 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3864         TCGA-AA-3866 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01Q         TCGA-AA-A024 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AY-4070         TCGA-AY-4071 
"15Q GAIN WILD-TYPE" "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 
                 1                147 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3538         TCGA-AA-3542 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3543         TCGA-AA-3544         TCGA-AA-3548 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3552         TCGA-AA-3553 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3555         TCGA-AA-3556 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3560         TCGA-AA-3561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3664         TCGA-AA-3666 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3675         TCGA-AA-3678         TCGA-AA-3679 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3715         TCGA-AA-3811 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3841 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3864         TCGA-AA-3866 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01Q         TCGA-AA-A024 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AY-4070         TCGA-AY-4071 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                170
  CLUS_2                3                184
  CLUS_3                1                 31
  CLUS_4                1                 23
D27V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                103
  CLUS_2                2                 84
  CLUS_3                0                 63
D27V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                116
  CLUS_3                1                  6
  CLUS_4                0                 76
D27V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                141
  CLUS_2                2                 21
  CLUS_3                0                 48
  CLUS_4                1                 50
D27V7, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                183 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3538 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3560         TCGA-AA-3561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3664         TCGA-AA-3666 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3678         TCGA-AA-3679         TCGA-AA-3680 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3684         TCGA-AA-3688 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3864 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3977 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3982         TCGA-AA-3984 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02R         TCGA-AA-A02W         TCGA-AA-A03F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AY-4070         TCGA-AY-4071 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AZ-4308         TCGA-AZ-4313         TCGA-AZ-4315 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AZ-4614         TCGA-AZ-4615         TCGA-AZ-4681 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AZ-4684         TCGA-CA-5256         TCGA-CK-4951 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4748 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CM-4750         TCGA-CM-4752         TCGA-CM-5341 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V8, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                183 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3538 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3560         TCGA-AA-3561 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3664         TCGA-AA-3666 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3678         TCGA-AA-3679         TCGA-AA-3680 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3684         TCGA-AA-3688 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3864 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3977 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3982         TCGA-AA-3984 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A02R         TCGA-AA-A02W         TCGA-AA-A03F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AY-4070         TCGA-AY-4071 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AZ-4308         TCGA-AZ-4313         TCGA-AZ-4315 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AZ-4614         TCGA-AZ-4615         TCGA-AZ-4681 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AZ-4684         TCGA-CA-5256         TCGA-CK-4951 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4748 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CM-4750         TCGA-CM-4752         TCGA-CM-5341 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V9, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                173
  CLUS_2                3                160
  CLUS_3                1                 60
D27V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                171
  CLUS_2                1                 43
  CLUS_3                3                179

Clustering(28) Variable = 16p gain mutation analysis
D28V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               17                 46
  CLUS_2                3                 29
  CLUS_3                2                 28
  CLUS_4                8                 15
D28V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 40
  CLUS_2                8                 40
  CLUS_3                2                 11
  CLUS_4               16                 27
D28V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               56                114
  CLUS_2                5                182
  CLUS_3                5                 27
  CLUS_4                1                 23
D28V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               20                 85
  CLUS_2                8                 78
  CLUS_3                7                 56
D28V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                 58
  CLUS_2               24                 93
  CLUS_3                1                  6
  CLUS_4               12                 64
D28V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               29                113
  CLUS_2                0                 23
  CLUS_3                8                 40
  CLUS_4                6                 45
D28V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               20                 47
  CLUS_2                6                 52
  CLUS_3                5                 34
  CLUS_4                7                 13
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                6                 12
  CLUS_3               29                 73
D28V9, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               36                138
  CLUS_2               21                142
  CLUS_3                8                 53
D28V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               37                135
  CLUS_2                4                 40
  CLUS_3               24                158

Clustering(29) Variable = 16q gain mutation analysis
D29V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               16                 47
  CLUS_2                2                 30
  CLUS_3                2                 28
  CLUS_4                7                 16
D29V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 41
  CLUS_2                8                 40
  CLUS_3                2                 11
  CLUS_4               14                 29
D29V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               58                112
  CLUS_2                4                183
  CLUS_3                3                 29
  CLUS_4                1                 23
D29V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               21                 84
  CLUS_2                9                 77
  CLUS_3                7                 56
D29V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                 58
  CLUS_2               25                 92
  CLUS_3                1                  6
  CLUS_4               11                 65
D29V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               29                113
  CLUS_2                0                 23
  CLUS_3                8                 40
  CLUS_4                6                 45
D29V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               20                 47
  CLUS_2                4                 54
  CLUS_3                5                 34
  CLUS_4                6                 14
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                5                 13
  CLUS_3               27                 75
D29V9, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               33                141
  CLUS_2               21                142
  CLUS_3               10                 51
D29V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               34                138
  CLUS_2                5                 39
  CLUS_3               25                157

Clustering(30) Variable = 17p gain mutation analysis
D30V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                146 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3675         TCGA-AA-3678 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3814         TCGA-AA-3818 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3841 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3979         TCGA-AA-3982 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01C         TCGA-AA-A01D         TCGA-AA-A01F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A024         TCGA-AA-A029 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02R         TCGA-AA-A02W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                146 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3675         TCGA-AA-3678 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3814         TCGA-AA-3818 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3841 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3979         TCGA-AA-3982 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01C         TCGA-AA-A01D         TCGA-AA-A01F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A024         TCGA-AA-A029 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02R         TCGA-AA-A02W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                167
  CLUS_2                5                182
  CLUS_3                0                 32
  CLUS_4                1                 23
D30V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                102
  CLUS_2                3                 83
  CLUS_3                1                 62
D30V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                3                114
  CLUS_3                0                  7
  CLUS_4                1                 75
D30V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                140
  CLUS_2                0                 23
  CLUS_3                1                 47
  CLUS_4                4                 47
D30V7, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                182 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3848         TCGA-AA-3850 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3864         TCGA-AA-3866 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02O         TCGA-AA-A02R 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A03F         TCGA-AA-A03J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AZ-4308 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4315         TCGA-AZ-4614 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AZ-4615         TCGA-AZ-4681         TCGA-AZ-4684 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CA-5256         TCGA-CK-4951         TCGA-CM-4746 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4748         TCGA-CM-4750 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V8, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                182 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3848         TCGA-AA-3850 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3864         TCGA-AA-3866 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02O         TCGA-AA-A02R 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A03F         TCGA-AA-A03J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AZ-4308 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4315         TCGA-AZ-4614 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AZ-4615         TCGA-AZ-4681         TCGA-AZ-4684 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CA-5256         TCGA-CK-4951         TCGA-CM-4746 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4748         TCGA-CM-4750 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V9, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                171
  CLUS_2                5                158
  CLUS_3                1                 60
D30V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                169
  CLUS_2                1                 43
  CLUS_3                5                177

Clustering(31) Variable = 17q gain mutation analysis
D31V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                 54
  CLUS_2                0                 32
  CLUS_3                2                 28
  CLUS_4                3                 20
D31V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                4                 44
  CLUS_3                0                 13
  CLUS_4                9                 34
D31V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               31                139
  CLUS_2               10                177
  CLUS_3                3                 29
  CLUS_4                4                 20
D31V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               20                 85
  CLUS_2               11                 75
  CLUS_3                2                 61
D31V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                 59
  CLUS_2               20                 97
  CLUS_3                0                  7
  CLUS_4                8                 68
D31V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               22                120
  CLUS_2                0                 23
  CLUS_3                5                 43
  CLUS_4                6                 45
D31V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               12                 55
  CLUS_2                0                 58
  CLUS_3                2                 37
  CLUS_4                4                 16
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                1                 17
  CLUS_3               16                 86
D31V9, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               18                156
  CLUS_2               26                137
  CLUS_3                3                 58
D31V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               18                154
  CLUS_2                5                 39
  CLUS_3               24                158

Clustering(32) Variable = 18p gain mutation analysis
D32V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 63
  CLUS_2                1                 31
  CLUS_3                2                 28
  CLUS_4                0                 23
D32V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                2                 46
  CLUS_3                0                 13
  CLUS_4                0                 43
D32V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                169
  CLUS_2               10                177
  CLUS_3                1                 31
  CLUS_4                3                 21
D32V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                104
  CLUS_2                8                 78
  CLUS_3                2                 61
D32V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                3                114
  CLUS_3                1                  6
  CLUS_4                3                 73
D32V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                138
  CLUS_2                1                 22
  CLUS_3                2                 46
  CLUS_4                3                 48
D32V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 67
  CLUS_2                3                 55
  CLUS_3                1                 38
  CLUS_4                0                 20
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                0                 18
  CLUS_3                0                102
D32V9, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                170
  CLUS_2               10                153
  CLUS_3                1                 60
D32V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                168
  CLUS_2                2                 42
  CLUS_3                9                173

Clustering(33) Variable = 18q gain mutation analysis
D33V1, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                147 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3666 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3675         TCGA-AA-3678         TCGA-AA-3679 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3715         TCGA-AA-3811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3818 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3841 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3864         TCGA-AA-3866 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01Q         TCGA-AA-A024 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AY-4070         TCGA-AY-4071 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                147 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3666 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3675         TCGA-AA-3678         TCGA-AA-3679 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3710         TCGA-AA-3715         TCGA-AA-3811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3818 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3819         TCGA-AA-3821         TCGA-AA-3831 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3837         TCGA-AA-3841 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3864         TCGA-AA-3866 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3867         TCGA-AA-3869         TCGA-AA-3870 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3875         TCGA-AA-3877 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01Q         TCGA-AA-A024 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02E         TCGA-AA-A02F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AY-4070         TCGA-AY-4071 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                170
  CLUS_2                8                179
  CLUS_3                1                 31
  CLUS_4                0                 24
D33V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                105
  CLUS_2                5                 81
  CLUS_3                2                 61
D33V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                1                116
  CLUS_3                1                  6
  CLUS_4                2                 74
D33V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                141
  CLUS_2                1                 22
  CLUS_3                2                 46
  CLUS_4                3                 48
D33V7, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                182 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3666 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3678         TCGA-AA-3679         TCGA-AA-3680 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3684         TCGA-AA-3688 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3977 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3982         TCGA-AA-3984 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A024         TCGA-AA-A029 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02O         TCGA-AA-A02R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A03F         TCGA-AA-A03J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AZ-4308 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4315         TCGA-AZ-4614 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AZ-4615         TCGA-AZ-4681         TCGA-AZ-4684 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CA-5256         TCGA-CK-4951         TCGA-CM-4746 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4748         TCGA-CM-4750 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V8, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                182 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3666 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3667         TCGA-AA-3672         TCGA-AA-3673 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3678         TCGA-AA-3679         TCGA-AA-3680 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3684         TCGA-AA-3688 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3977 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3982         TCGA-AA-3984 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A024         TCGA-AA-A029 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02O         TCGA-AA-A02R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A03F         TCGA-AA-A03J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AZ-4308 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4315         TCGA-AZ-4614 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AZ-4615         TCGA-AZ-4681         TCGA-AZ-4684 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CA-5256         TCGA-CK-4951         TCGA-CM-4746 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4748         TCGA-CM-4750 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V9, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                172
  CLUS_2                6                157
  CLUS_3                1                 60
D33V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                170
  CLUS_2                1                 43
  CLUS_3                6                176

Clustering(34) Variable = 19p gain mutation analysis
D34V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                6                 57
  CLUS_2                0                 32
  CLUS_3                5                 25
  CLUS_4                1                 22
D34V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                4                 44
  CLUS_3                2                 11
  CLUS_4                5                 38
D34V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               18                152
  CLUS_2                7                180
  CLUS_3                5                 27
  CLUS_4                4                 20
D34V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               10                 95
  CLUS_2               10                 76
  CLUS_3                1                 62
D34V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                5                 59
  CLUS_2               13                104
  CLUS_3                1                  6
  CLUS_4                3                 73
D34V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               16                126
  CLUS_2                0                 23
  CLUS_3                2                 46
  CLUS_4                4                 47
D34V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                6                 61
  CLUS_2                3                 55
  CLUS_3                4                 35
  CLUS_4                1                 19
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                3                 15
  CLUS_3                9                 93
D34V9, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               11                163
  CLUS_2               15                148
  CLUS_3                5                 56
D34V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               13                159
  CLUS_2                5                 39
  CLUS_3               13                169

Clustering(35) Variable = 19q gain mutation analysis
D35V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                 56
  CLUS_2                0                 32
  CLUS_3                5                 25
  CLUS_4                1                 22
D35V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                5                 43
  CLUS_3                3                 10
  CLUS_4                4                 39
D35V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               18                152
  CLUS_2               15                172
  CLUS_3                4                 28
  CLUS_4                4                 20
D35V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               13                 92
  CLUS_2               12                 74
  CLUS_3                2                 61
D35V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                6                 58
  CLUS_2               20                 97
  CLUS_3                1                  6
  CLUS_4                3                 73
D35V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               23                119
  CLUS_2                1                 22
  CLUS_3                2                 46
  CLUS_4                4                 47
D35V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                8                 59
  CLUS_2                1                 57
  CLUS_3                9                 30
  CLUS_4                1                 19
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                2                 16
  CLUS_3               13                 89
D35V9, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               17                157
  CLUS_2               16                147
  CLUS_3                7                 54
D35V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               17                155
  CLUS_2                5                 39
  CLUS_3               18                164

Clustering(36) Variable = 20p gain mutation analysis
D36V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               38                 25
  CLUS_2                9                 23
  CLUS_3               11                 19
  CLUS_4               16                  7
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                8                 36
  CLUS_2               31                 17
  CLUS_3                8                  5
  CLUS_4               27                 16
D36V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               98                 72
  CLUS_2               44                143
  CLUS_3               31                  1
  CLUS_4               15                  9
D36V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               57                 48
  CLUS_2               30                 56
  CLUS_3               23                 40
D36V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               37                 27
  CLUS_2               46                 71
  CLUS_3                4                  3
  CLUS_4               26                 50
D36V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               61                 81
  CLUS_2                8                 15
  CLUS_3               15                 33
  CLUS_4               29                 22
D36V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               44                 23
  CLUS_2               14                 44
  CLUS_3               18                 21
  CLUS_4               14                  6
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                 49
  CLUS_2                8                 10
  CLUS_3               67                 35
D36V9, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               88                 86
  CLUS_2               71                 92
  CLUS_3               23                 38
D36V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               88                 84
  CLUS_2               22                 22
  CLUS_3               72                110

Clustering(37) Variable = 20q gain mutation analysis
D37V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               59                  4
  CLUS_2               10                 22
  CLUS_3               13                 17
  CLUS_4               19                  4
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                 34
  CLUS_2               43                  5
  CLUS_3                8                  5
  CLUS_4               40                  3
D37V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              160                 10
  CLUS_2               54                133
  CLUS_3               32                  0
  CLUS_4               21                  3
D37V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               89                 16
  CLUS_2               37                 49
  CLUS_3               33                 30
D37V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               47                 17
  CLUS_2               81                 36
  CLUS_3                4                  3
  CLUS_4               34                 42
D37V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               97                 45
  CLUS_2               10                 13
  CLUS_3               18                 30
  CLUS_4               41                 10
D37V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               64                  3
  CLUS_2               17                 41
  CLUS_3               23                 16
  CLUS_4               18                  2
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               17                 47
  CLUS_2               12                  6
  CLUS_3               93                  9
D37V9, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              117                 57
  CLUS_2              108                 55
  CLUS_3               32                 29
D37V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1              117                 55
  CLUS_2               28                 16
  CLUS_3              112                 70

Clustering(38) Variable = 21q gain mutation analysis
D38V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 61
  CLUS_2                0                 32
  CLUS_3                0                 30
  CLUS_4                2                 21
D38V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                1                 47
  CLUS_3                0                 13
  CLUS_4                3                 40
D38V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                9                161
  CLUS_2                2                185
  CLUS_3                0                 32
  CLUS_4                0                 24
D38V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                101
  CLUS_2                3                 83
  CLUS_3                0                 63
D38V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                6                111
  CLUS_3                0                  7
  CLUS_4                1                 75
D38V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                6                136
  CLUS_2                0                 23
  CLUS_3                1                 47
  CLUS_4                0                 51
D38V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                1                 57
  CLUS_3                0                 39
  CLUS_4                0                 20
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 18
  CLUS_3                3                 99
D38V9, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                170
  CLUS_2                6                157
  CLUS_3                1                 60
D38V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                168
  CLUS_2                2                 42
  CLUS_3                5                177

Clustering(39) Variable = Xq gain mutation analysis
D39V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                63
  CLUS_2               0                32
  CLUS_3               2                28
  CLUS_4               1                22
D39V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                44
  CLUS_2               2                46
  CLUS_3               0                13
  CLUS_4               1                42
D39V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4               166
  CLUS_2               3               184
  CLUS_3               3                29
  CLUS_4               2                22
D39V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               4               101
  CLUS_2               4                82
  CLUS_3               1                62
D39V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                61
  CLUS_2               7               110
  CLUS_3               0                 7
  CLUS_4               0                76
D39V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               7               135
  CLUS_2               0                23
  CLUS_3               0                48
  CLUS_4               3                48
D39V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                66
  CLUS_2               2                56
  CLUS_3               1                38
  CLUS_4               0                20
D39V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                62
  CLUS_2               1                17
  CLUS_3               1               101
D39V9, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               171
  CLUS_2               7               156
  CLUS_3               1                60
D39V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3               169
  CLUS_2               2                42
  CLUS_3               6               176

Clustering(40) Variable = 1p loss mutation analysis
D40V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              17                46
  CLUS_2               1                31
  CLUS_3               1                29
  CLUS_4               3                20
D40V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2              12                36
  CLUS_3               3                10
  CLUS_4               7                36
D40V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              36               134
  CLUS_2               6               181
  CLUS_3               8                24
  CLUS_4               1                23
D40V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              20                85
  CLUS_2               4                82
  CLUS_3               4                59
D40V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               7                57
  CLUS_2              16               101
  CLUS_3               1                 6
  CLUS_4               7                69
D40V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              20               122
  CLUS_2               3                20
  CLUS_3               4                44
  CLUS_4               4                47
D40V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              17                50
  CLUS_2               2                56
  CLUS_3               5                34
  CLUS_4               3                17
D40V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               3                15
  CLUS_3              22                80
D40V9, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              23               151
  CLUS_2              21               142
  CLUS_3               3                58
D40V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              21               151
  CLUS_2               2                42
  CLUS_3              24               158

Clustering(41) Variable = 1q loss mutation analysis
D41V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6                57
  CLUS_2               0                32
  CLUS_3               1                29
  CLUS_4               1                22
D41V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               5                43
  CLUS_3               1                12
  CLUS_4               2                41
D41V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              11               159
  CLUS_2               3               184
  CLUS_3               4                28
  CLUS_4               0                24
D41V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               6                99
  CLUS_2               1                85
  CLUS_3               3                60
D41V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               6               111
  CLUS_3               1                 6
  CLUS_4               2                74
D41V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               135
  CLUS_2               2                21
  CLUS_3               2                46
  CLUS_4               1                50
D41V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               5                62
  CLUS_2               1                57
  CLUS_3               2                37
  CLUS_4               2                18
D41V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                64
  CLUS_2               1                17
  CLUS_3               9                93
D41V9, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               8               166
  CLUS_2               6               157
  CLUS_3               2                59
D41V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               8               164
  CLUS_2               0                44
  CLUS_3               8               174

Clustering(42) Variable = 2p loss mutation analysis
D42V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                61
  CLUS_2               0                32
  CLUS_3               0                30
  CLUS_4               1                22
D42V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               2                46
  CLUS_3               1                12
  CLUS_4               0                43
D42V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2               168
  CLUS_2               1               186
  CLUS_3               1                31
  CLUS_4               0                24
D42V4, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1               253 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2675        TCGA-A6-2679 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2684 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-4105        TCGA-A6-4107 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137        TCGA-A6-6138 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142        TCGA-A6-6648 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651        TCGA-A6-6652 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6782        TCGA-AA-3488        TCGA-AA-3489        TCGA-AA-3492 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3494        TCGA-AA-3495        TCGA-AA-3496        TCGA-AA-3502 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3506        TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3655 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3660        TCGA-AA-3662        TCGA-AA-3663        TCGA-AA-3697 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3712        TCGA-AA-3713        TCGA-AD-5900        TCGA-AD-6548 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6965        TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4308        TCGA-AZ-4313        TCGA-AZ-4315 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-5256        TCGA-CA-5796        TCGA-CA-6715        TCGA-CA-6716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4951        TCGA-CK-4952 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750        TCGA-CM-4751 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532        TCGA-D5-6533 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280        TCGA-DM-A282 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A285        TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6294 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298        TCGA-G4-6299 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6311 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6586 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6627 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6628 
"2P LOSS WILD-TYPE" 
D42V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               262 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2676        TCGA-A6-2677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-3807 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-3810        TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AA-3489        TCGA-AA-3492 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3496        TCGA-AA-3502        TCGA-AA-3506        TCGA-AA-3510 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3519 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3525 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3548        TCGA-AA-3552        TCGA-AA-3553 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3555        TCGA-AA-3558        TCGA-AA-3561 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3664        TCGA-AA-3672 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3681        TCGA-AA-3688        TCGA-AA-3695 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3831 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841        TCGA-AA-3844 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3845        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3852 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3856        TCGA-AA-3864        TCGA-AA-3866 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3869        TCGA-AA-3872        TCGA-AA-3930        TCGA-AA-3947 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3955        TCGA-AA-3968        TCGA-AA-3971 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3982 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AD-5900        TCGA-AD-6548 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6899        TCGA-AD-6965        TCGA-AM-5820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AM-5821        TCGA-AU-6004        TCGA-AY-5543        TCGA-AY-6196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4308        TCGA-AZ-4315 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5407        TCGA-AZ-6598 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-5914        TCGA-CK-5916        TCGA-CK-6746 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4750        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5538 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532        TCGA-D5-6533 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-F4-6459 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6294        TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6311        TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6320        TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6627        TCGA-G4-6628 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D42V6, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               262 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2676        TCGA-A6-2677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2678        TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-3807 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-3810        TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5660        TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-5665        TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6138        TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AA-3489        TCGA-AA-3492 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3496        TCGA-AA-3502        TCGA-AA-3506        TCGA-AA-3510 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517        TCGA-AA-3519 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3525 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3548        TCGA-AA-3552        TCGA-AA-3553 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3554        TCGA-AA-3555        TCGA-AA-3558        TCGA-AA-3561 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3664        TCGA-AA-3672 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3681        TCGA-AA-3688        TCGA-AA-3695 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3831 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841        TCGA-AA-3844 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3845        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3852 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3856        TCGA-AA-3864        TCGA-AA-3866 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3869        TCGA-AA-3872        TCGA-AA-3930        TCGA-AA-3947 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3955        TCGA-AA-3968        TCGA-AA-3971 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3982 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AD-5900        TCGA-AD-6548 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6899        TCGA-AD-6965        TCGA-AM-5820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AM-5821        TCGA-AU-6004        TCGA-AY-5543        TCGA-AY-6196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4308        TCGA-AZ-4315 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5407        TCGA-AZ-6598 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5256        TCGA-CA-5796 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-5914        TCGA-CK-5916        TCGA-CK-6746 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-4750        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5538 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532        TCGA-D5-6533 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-F4-6459 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6294        TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6311        TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6320        TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G4-6627        TCGA-G4-6628 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D42V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               1                57
  CLUS_3               2                37
  CLUS_4               0                20
D42V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               0                18
  CLUS_3               2               100
D42V9, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               171
  CLUS_2               1               162
  CLUS_3               0                61
D42V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3               169
  CLUS_2               1                43
  CLUS_3               0               182

Clustering(43) Variable = 2q loss mutation analysis
D43V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                61
  CLUS_2               1                31
  CLUS_3               1                29
  CLUS_4               1                22
D43V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               2                46
  CLUS_3               2                11
  CLUS_4               0                43
D43V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3               167
  CLUS_2               2               185
  CLUS_3               1                31
  CLUS_4               0                24
D43V4, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               253 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2675        TCGA-A6-2679 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2684 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-2685        TCGA-A6-2686        TCGA-A6-4105        TCGA-A6-4107 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-5667        TCGA-A6-6137        TCGA-A6-6138 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6140        TCGA-A6-6141        TCGA-A6-6142        TCGA-A6-6648 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6649        TCGA-A6-6650        TCGA-A6-6651        TCGA-A6-6652 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780        TCGA-A6-6781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A6-6782        TCGA-AA-3488        TCGA-AA-3489        TCGA-AA-3492 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AA-3494        TCGA-AA-3495        TCGA-AA-3496        TCGA-AA-3502 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AA-3506        TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3655 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AA-3660        TCGA-AA-3662        TCGA-AA-3663        TCGA-AA-3697 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AA-3712        TCGA-AA-3713        TCGA-AD-5900        TCGA-AD-6548 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AD-6965        TCGA-AM-5820        TCGA-AM-5821        TCGA-AU-3779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4308        TCGA-AZ-4313        TCGA-AZ-4315 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4614        TCGA-AZ-4615        TCGA-AZ-4616 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-4684        TCGA-AZ-5403 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-5256        TCGA-CA-5796        TCGA-CA-6715        TCGA-CA-6716 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4951        TCGA-CK-4952 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750        TCGA-CM-4751 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6530        TCGA-D5-6531        TCGA-D5-6532        TCGA-D5-6533 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A280        TCGA-DM-A282 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A285        TCGA-DM-A288        TCGA-DM-A28A        TCGA-DM-A28C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DM-A28K        TCGA-DM-A28M        TCGA-F4-6459        TCGA-F4-6460 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6461        TCGA-F4-6463        TCGA-F4-6569        TCGA-F4-6570 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6294 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6295        TCGA-G4-6297        TCGA-G4-6298        TCGA-G4-6299 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6302        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6314        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6320 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6321        TCGA-G4-6322        TCGA-G4-6323        TCGA-G4-6586 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6627 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G4-6628 
"2Q LOSS WILD-TYPE" 
D43V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               1               116
  CLUS_3               1                 6
  CLUS_4               0                76
D43V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1               141
  CLUS_2               1                22
  CLUS_3               0                48
  CLUS_4               1                50
D43V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                67
  CLUS_2               2                56
  CLUS_3               3                36
  CLUS_4               0                20
D43V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                18
  CLUS_3               3                99
D43V9, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               169
  CLUS_2               1               162
  CLUS_3               0                61
D43V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5               167
  CLUS_2               1                43
  CLUS_3               0               182

Clustering(44) Variable = 3p loss mutation analysis
D44V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               8                55
  CLUS_2               1                31
  CLUS_3               2                28
  CLUS_4               2                21
D44V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               5                43
  CLUS_3               2                11
  CLUS_4               5                38
D44V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              18               152
  CLUS_2               4               183
  CLUS_3               4                28
  CLUS_4               1                23
D44V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9                96
  CLUS_2               3                83
  CLUS_3               2                61
D44V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               6               111
  CLUS_3               1                 6
  CLUS_4               5                71
D44V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               8               134
  CLUS_2               1                22
  CLUS_3               3                45
  CLUS_4               2                49
D44V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               8                59
  CLUS_2               4                54
  CLUS_3               3                36
  CLUS_4               1                19
D44V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               3                15
  CLUS_3              10                92
D44V9, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              14               160
  CLUS_2              10               153
  CLUS_3               1                60
D44V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              14               158
  CLUS_2               4                40
  CLUS_3               7               175

Clustering(45) Variable = 3q loss mutation analysis
D45V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                60
  CLUS_2               1                31
  CLUS_3               1                29
  CLUS_4               2                21
D45V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                43
  CLUS_2               3                45
  CLUS_3               1                12
  CLUS_4               2                41
D45V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               7               163
  CLUS_2               3               184
  CLUS_3               2                30
  CLUS_4               0                24
D45V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2               103
  CLUS_2               2                84
  CLUS_3               1                62
D45V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                64
  CLUS_2               3               114
  CLUS_3               1                 6
  CLUS_4               1                75
D45V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               4               138
  CLUS_2               1                22
  CLUS_3               0                48
  CLUS_4               0                51
D45V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                64
  CLUS_2               2                56
  CLUS_3               1                38
  CLUS_4               1                19
D45V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               2                16
  CLUS_3               4                98
D45V9, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               6               168
  CLUS_2               5               158
  CLUS_3               0                61
D45V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               6               166
  CLUS_2               1                43
  CLUS_3               4               178

Clustering(46) Variable = 4p loss mutation analysis
D46V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              23                40
  CLUS_2               6                26
  CLUS_3               1                29
  CLUS_4               7                16
D46V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                39
  CLUS_2              16                32
  CLUS_3               2                11
  CLUS_4              14                29
D46V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              56               114
  CLUS_2              11               176
  CLUS_3              13                19
  CLUS_4               4                20
D46V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              29                76
  CLUS_2               9                77
  CLUS_3               7                56
D46V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9                55
  CLUS_2              25                92
  CLUS_3               3                 4
  CLUS_4              11                65
D46V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              31               111
  CLUS_2               5                18
  CLUS_3               5                43
  CLUS_4               7                44
D46V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              25                42
  CLUS_2              11                47
  CLUS_3               4                35
  CLUS_4               6                14
D46V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9                55
  CLUS_2               7                11
  CLUS_3              30                72
D46V9, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              39               135
  CLUS_2              34               129
  CLUS_3               6                55
D46V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              39               133
  CLUS_2              10                34
  CLUS_3              30               152

Clustering(47) Variable = 4q loss mutation analysis
D47V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              21                42
  CLUS_2               5                27
  CLUS_3               1                29
  CLUS_4               6                17
D47V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4                40
  CLUS_2              15                33
  CLUS_3               1                12
  CLUS_4              13                30
D47V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              49               121
  CLUS_2               8               179
  CLUS_3               9                23
  CLUS_4               2                22
D47V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              23                82
  CLUS_2               5                81
  CLUS_3               5                58
D47V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                56
  CLUS_2              20                97
  CLUS_3               3                 4
  CLUS_4               8                68
D47V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              25               117
  CLUS_2               5                18
  CLUS_3               4                44
  CLUS_4               5                46
D47V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              21                46
  CLUS_2               9                49
  CLUS_3               5                34
  CLUS_4               7                13
D47V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              10                54
  CLUS_2               4                14
  CLUS_3              28                74
D47V9, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              36               138
  CLUS_2              26               137
  CLUS_3               2                59
D47V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              37               135
  CLUS_2               6                38
  CLUS_3              21               161

Clustering(48) Variable = 5p loss mutation analysis
D48V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               6                57
  CLUS_2               1                31
  CLUS_3               1                29
  CLUS_4               1                22
D48V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               1                47
  CLUS_3               2                11
  CLUS_4               4                39
D48V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              18               152
  CLUS_2               3               184
  CLUS_3               2                30
  CLUS_4               2                22
D48V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10                95
  CLUS_2               2                84
  CLUS_3               3                60
D48V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                59
  CLUS_2               9               108
  CLUS_3               0                 7
  CLUS_4               3                73
D48V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10               132
  CLUS_2               0                23
  CLUS_3               3                45
  CLUS_4               4                47
D48V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               7                60
  CLUS_2               3                55
  CLUS_3               3                36
  CLUS_4               0                20
D48V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               2                16
  CLUS_3               8                94
D48V9, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               9               165
  CLUS_2              11               152
  CLUS_3               3                58
D48V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10               162
  CLUS_2               3                41
  CLUS_3              10               172

Clustering(49) Variable = 5q loss mutation analysis
D49V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              10                53
  CLUS_2               3                29
  CLUS_3               0                30
  CLUS_4               3                20
D49V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                41
  CLUS_2               3                45
  CLUS_3               1                12
  CLUS_4               9                34
D49V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              27               143
  CLUS_2               4               183
  CLUS_3               3                29
  CLUS_4               4                20
D49V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              11                94
  CLUS_2               4                82
  CLUS_3               6                57
D49V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7                57
  CLUS_2               8               109
  CLUS_3               1                 6
  CLUS_4               4                72
D49V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8               134
  CLUS_2               1                22
  CLUS_3               4                44
  CLUS_4               7                44
D49V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              13                54
  CLUS_2               4                54
  CLUS_3               1                38
  CLUS_4               3                17
D49V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2               3                15
  CLUS_3              15                87
D49V9, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              17               157
  CLUS_2              15               148
  CLUS_3               3                58
D49V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              17               155
  CLUS_2               5                39
  CLUS_3              13               169

Clustering(50) Variable = 6p loss mutation analysis
D50V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                60
  CLUS_2               0                32
  CLUS_3               2                28
  CLUS_4               1                22
D50V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               3                45
  CLUS_3               2                11
  CLUS_4               1                42
D50V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3               167
  CLUS_2               3               184
  CLUS_3               5                27
  CLUS_4               1                23
D50V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2               103
  CLUS_2               2                84
  CLUS_3               1                62
D50V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               4               113
  CLUS_3               0                 7
  CLUS_4               1                75
D50V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               5               137
  CLUS_2               0                23
  CLUS_3               1                47
  CLUS_4               1                50
D50V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                65
  CLUS_2               1                57
  CLUS_3               4                35
  CLUS_4               0                20
D50V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               0                18
  CLUS_3               6                96
D50V9, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6               168
  CLUS_2               3               160
  CLUS_3               2                59
D50V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6               166
  CLUS_2               0                44
  CLUS_3               5               177

Clustering(51) Variable = 6q loss mutation analysis
D51V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                57
  CLUS_2               2                30
  CLUS_3               2                28
  CLUS_4               1                22
D51V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                42
  CLUS_2               4                44
  CLUS_3               2                11
  CLUS_4               3                40
D51V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7               163
  CLUS_2               8               179
  CLUS_3               5                27
  CLUS_4               1                23
D51V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5               100
  CLUS_2               2                84
  CLUS_3               2                61
D51V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               4                60
  CLUS_2               5               112
  CLUS_3               1                 6
  CLUS_4               1                75
D51V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8               134
  CLUS_2               0                23
  CLUS_3               1                47
  CLUS_4               2                49
D51V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               4                63
  CLUS_2               4                54
  CLUS_3               4                35
  CLUS_4               0                20
D51V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               1                17
  CLUS_3               9                93
D51V9, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              10               164
  CLUS_2               7               156
  CLUS_3               3                58
D51V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               9               163
  CLUS_2               2                42
  CLUS_3               9               173

Clustering(52) Variable = 8p loss mutation analysis
D52V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              24                39
  CLUS_2               2                30
  CLUS_3               3                27
  CLUS_4               9                14
D52V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                40
  CLUS_2              13                35
  CLUS_3               5                 8
  CLUS_4              16                27
D52V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              73                97
  CLUS_2              11               176
  CLUS_3               3                29
  CLUS_4               6                18
D52V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              34                71
  CLUS_2              11                75
  CLUS_3               8                55
D52V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              14                50
  CLUS_2              33                84
  CLUS_3               1                 6
  CLUS_4              12                64
D52V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              38               104
  CLUS_2               4                19
  CLUS_3               4                44
  CLUS_4              14                37
D52V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              25                42
  CLUS_2               5                53
  CLUS_3               8                31
  CLUS_4               9                11
D52V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8                56
  CLUS_2               3                15
  CLUS_3              36                66
D52V9, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              45               129
  CLUS_2              36               127
  CLUS_3               9                52
D52V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              45               127
  CLUS_2               8                36
  CLUS_3              37               145

Clustering(53) Variable = 8q loss mutation analysis
D53V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                60
  CLUS_2               0                32
  CLUS_3               0                30
  CLUS_4               0                23
D53V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               2                46
  CLUS_3               0                13
  CLUS_4               1                42
D53V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               8               162
  CLUS_2               0               187
  CLUS_3               0                32
  CLUS_4               0                24
D53V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3               102
  CLUS_2               1                85
  CLUS_3               1                62
D53V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                63
  CLUS_2               5               112
  CLUS_3               0                 7
  CLUS_4               0                76
D53V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5               137
  CLUS_2               0                23
  CLUS_3               0                48
  CLUS_4               1                50
D53V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5                62
  CLUS_2               0                58
  CLUS_3               0                39
  CLUS_4               0                20
D53V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                64
  CLUS_2               2                16
  CLUS_3               3                99
D53V9, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5               169
  CLUS_2               1               162
  CLUS_3               2                59
D53V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               5               167
  CLUS_2               1                43
  CLUS_3               2               180

Clustering(54) Variable = 9p loss mutation analysis
D54V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                58
  CLUS_2               1                31
  CLUS_3               1                29
  CLUS_4               1                22
D54V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               4                44
  CLUS_3               1                12
  CLUS_4               3                40
D54V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              19               151
  CLUS_2               2               185
  CLUS_3               5                27
  CLUS_4               1                23
D54V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                94
  CLUS_2               2                84
  CLUS_3               5                58
D54V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2              13               104
  CLUS_3               0                 7
  CLUS_4               3                73
D54V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              14               128
  CLUS_2               0                23
  CLUS_3               1                47
  CLUS_4               4                47
D54V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               7                60
  CLUS_2               3                55
  CLUS_3               1                38
  CLUS_4               0                20
D54V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                60
  CLUS_2               0                18
  CLUS_3               7                95
D54V9, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              12               162
  CLUS_2              13               150
  CLUS_3               2                59
D54V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11               161
  CLUS_2               4                40
  CLUS_3              12               170

Clustering(55) Variable = 9q loss mutation analysis
D55V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                58
  CLUS_2               1                31
  CLUS_3               0                30
  CLUS_4               2                21
D55V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                44
  CLUS_2               3                45
  CLUS_3               1                12
  CLUS_4               4                39
D55V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              21               149
  CLUS_2               1               186
  CLUS_3               4                28
  CLUS_4               0                24
D55V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              13                92
  CLUS_2               0                86
  CLUS_3               4                59
D55V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                61
  CLUS_2              13               104
  CLUS_3               0                 7
  CLUS_4               3                73
D55V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              14               128
  CLUS_2               0                23
  CLUS_3               1                47
  CLUS_4               4                47
D55V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               8                59
  CLUS_2               1                57
  CLUS_3               1                38
  CLUS_4               0                20
D55V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                62
  CLUS_2               0                18
  CLUS_3               8                94
D55V9, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10               164
  CLUS_2              15               148
  CLUS_3               1                60
D55V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10               162
  CLUS_2               4                40
  CLUS_3              12               170

Clustering(56) Variable = 10p loss mutation analysis
D56V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 59
  CLUS_2                2                 30
  CLUS_3                0                 30
  CLUS_4                1                 22
D56V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                3                 45
  CLUS_3                1                 12
  CLUS_4                2                 41
D56V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                160
  CLUS_2                4                183
  CLUS_3                7                 25
  CLUS_4                1                 23
D56V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                8                 97
  CLUS_2                5                 81
  CLUS_3                1                 62
D56V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                7                110
  CLUS_3                2                  5
  CLUS_4                4                 72
D56V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                132
  CLUS_2                1                 22
  CLUS_3                3                 45
  CLUS_4                1                 50
D56V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                 61
  CLUS_2                3                 55
  CLUS_3                0                 39
  CLUS_4                1                 19
D56V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                3                 15
  CLUS_3                5                 97
D56V9, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                168
  CLUS_2               12                151
  CLUS_3                2                 59
D56V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                165
  CLUS_2                2                 42
  CLUS_3               11                171

Clustering(57) Variable = 10q loss mutation analysis
D57V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 57
  CLUS_2                2                 30
  CLUS_3                0                 30
  CLUS_4                1                 22
D57V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                4                 44
  CLUS_3                1                 12
  CLUS_4                3                 40
D57V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               14                156
  CLUS_2                3                184
  CLUS_3                6                 26
  CLUS_4                1                 23
D57V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                9                 96
  CLUS_2                4                 82
  CLUS_3                1                 62
D57V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                7                110
  CLUS_3                2                  5
  CLUS_4                3                 73
D57V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                9                133
  CLUS_2                1                 22
  CLUS_3                3                 45
  CLUS_4                2                 49
D57V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                 59
  CLUS_2                3                 55
  CLUS_3                1                 38
  CLUS_4                1                 19
D57V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                4                 14
  CLUS_3                7                 95
D57V9, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                166
  CLUS_2               11                152
  CLUS_3                3                 58
D57V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               10                162
  CLUS_2                4                 40
  CLUS_3                8                174

Clustering(58) Variable = 11p loss mutation analysis
D58V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                7                 56
  CLUS_2                1                 31
  CLUS_3                1                 29
  CLUS_4                1                 22
D58V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                5                 43
  CLUS_3                1                 12
  CLUS_4                4                 39
D58V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               14                156
  CLUS_2                2                185
  CLUS_3                6                 26
  CLUS_4                0                 24
D58V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 95
  CLUS_2                0                 86
  CLUS_3                0                 63
D58V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                5                112
  CLUS_3                0                  7
  CLUS_4                2                 74
D58V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                137
  CLUS_2                1                 22
  CLUS_3                2                 46
  CLUS_4                0                 51
D58V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 61
  CLUS_2                4                 54
  CLUS_3                2                 37
  CLUS_4                1                 19
D58V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                0                 18
  CLUS_3                8                 94
D58V9, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               14                160
  CLUS_2                8                155
  CLUS_3                0                 61
D58V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               13                159
  CLUS_2                3                 41
  CLUS_3                6                176

Clustering(59) Variable = 11q loss mutation analysis
D59V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 55
  CLUS_2                1                 31
  CLUS_3                1                 29
  CLUS_4                1                 22
D59V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                6                 42
  CLUS_3                1                 12
  CLUS_4                4                 39
D59V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               19                151
  CLUS_2                2                185
  CLUS_3                6                 26
  CLUS_4                0                 24
D59V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               14                 91
  CLUS_2                0                 86
  CLUS_3                0                 63
D59V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                6                111
  CLUS_3                0                  7
  CLUS_4                2                 74
D59V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                135
  CLUS_2                2                 21
  CLUS_3                2                 46
  CLUS_4                1                 50
D59V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 59
  CLUS_2                4                 54
  CLUS_3                2                 37
  CLUS_4                1                 19
D59V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                1                 17
  CLUS_3                9                 93
D59V9, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               15                159
  CLUS_2               10                153
  CLUS_3                2                 59
D59V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               15                157
  CLUS_2                4                 40
  CLUS_3                8                174

Clustering(60) Variable = 12p loss mutation analysis
D60V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                7                 56
  CLUS_2                1                 31
  CLUS_3                0                 30
  CLUS_4                0                 23
D60V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                5                 43
  CLUS_3                0                 13
  CLUS_4                3                 40
D60V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               17                153
  CLUS_2                1                186
  CLUS_3                3                 29
  CLUS_4                0                 24
D60V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                 97
  CLUS_2                3                 83
  CLUS_3                1                 62
D60V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                7                110
  CLUS_3                1                  6
  CLUS_4                3                 73
D60V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                134
  CLUS_2                1                 22
  CLUS_3                3                 45
  CLUS_4                2                 49
D60V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                 59
  CLUS_2                3                 55
  CLUS_3                2                 37
  CLUS_4                0                 20
D60V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                2                 16
  CLUS_3                7                 95
D60V9, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               11                163
  CLUS_2                7                156
  CLUS_3                3                 58
D60V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               13                159
  CLUS_2                2                 42
  CLUS_3                6                176

Clustering(61) Variable = 12q loss mutation analysis
D61V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                6                 57
  CLUS_2                2                 30
  CLUS_3                0                 30
  CLUS_4                0                 23
D61V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                4                 44
  CLUS_3                0                 13
  CLUS_4                4                 39
D61V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               15                155
  CLUS_2                1                186
  CLUS_3                4                 28
  CLUS_4                0                 24
D61V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                 97
  CLUS_2                2                 84
  CLUS_3                1                 62
D61V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                5                112
  CLUS_3                0                  7
  CLUS_4                3                 73
D61V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                7                135
  CLUS_2                1                 22
  CLUS_3                3                 45
  CLUS_4                2                 49
D61V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                7                 60
  CLUS_2                3                 55
  CLUS_3                2                 37
  CLUS_4                0                 20
D61V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                1                 17
  CLUS_3                8                 94
D61V9, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               11                163
  CLUS_2                8                155
  CLUS_3                1                 60
D61V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               12                160
  CLUS_2                1                 43
  CLUS_3                7                175

Clustering(62) Variable = 13q loss mutation analysis
D62V1, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                146 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3675         TCGA-AA-3678 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3877 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A024         TCGA-AA-A029 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02R         TCGA-AA-A02W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D62V2, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                146 
        TCGA-A6-2670         TCGA-A6-2672         TCGA-A6-2674 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3810 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3516         TCGA-AA-3517 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3675         TCGA-AA-3678 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3710         TCGA-AA-3715 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3841         TCGA-AA-3842         TCGA-AA-3844 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3877 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3930         TCGA-AA-3939         TCGA-AA-3941 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3947         TCGA-AA-3949         TCGA-AA-3950 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3952         TCGA-AA-3955         TCGA-AA-3956 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3966         TCGA-AA-3968         TCGA-AA-3971 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3977         TCGA-AA-3979 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01C         TCGA-AA-A01F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A024         TCGA-AA-A029 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02R         TCGA-AA-A02W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D62V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                169
  CLUS_2                2                185
  CLUS_3                3                 29
  CLUS_4                0                 24
D62V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                103
  CLUS_2                0                 86
  CLUS_3                2                 61
D62V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 61
  CLUS_2                0                117
  CLUS_3                0                  7
  CLUS_4                0                 76
D62V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                142
  CLUS_2                0                 23
  CLUS_3                0                 48
  CLUS_4                3                 48
D62V7, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                182 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3812 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3814         TCGA-AA-3818         TCGA-AA-3819 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3841         TCGA-AA-3842 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3845         TCGA-AA-3846 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3977 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3982         TCGA-AA-3984 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02O         TCGA-AA-A02R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A03F         TCGA-AA-A03J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AZ-4308 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4315         TCGA-AZ-4614 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AZ-4615         TCGA-AZ-4681         TCGA-AZ-4684 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CA-5256         TCGA-CK-4951         TCGA-CM-4746 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4748         TCGA-CM-4750 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D62V8, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                182 
        TCGA-A6-2670         TCGA-A6-2671         TCGA-A6-2672 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2674         TCGA-A6-2676         TCGA-A6-2677 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2678         TCGA-A6-2679         TCGA-A6-2680 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2682         TCGA-A6-2683 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-2684         TCGA-A6-2685         TCGA-A6-3807 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A6-3810         TCGA-A6-4107         TCGA-AA-3488 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3494         TCGA-AA-3495 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3514 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3516         TCGA-AA-3517         TCGA-AA-3518 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3664 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3688         TCGA-AA-3692         TCGA-AA-3693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3695         TCGA-AA-3696         TCGA-AA-3710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3715         TCGA-AA-3811         TCGA-AA-3812 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3814         TCGA-AA-3818         TCGA-AA-3819 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3841         TCGA-AA-3842 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3844         TCGA-AA-3845         TCGA-AA-3846 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3848         TCGA-AA-3850         TCGA-AA-3851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3855 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3856         TCGA-AA-3858         TCGA-AA-3860 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3966         TCGA-AA-3968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3977 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3982         TCGA-AA-3984 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02E         TCGA-AA-A02F         TCGA-AA-A02H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02O         TCGA-AA-A02R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A03F         TCGA-AA-A03J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AZ-4308 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AZ-4313         TCGA-AZ-4315         TCGA-AZ-4614 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AZ-4615         TCGA-AZ-4681         TCGA-AZ-4684 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CA-5256         TCGA-CK-4951         TCGA-CM-4746 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4748         TCGA-CM-4750 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D62V9, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                172
  CLUS_2                3                160
  CLUS_3                1                 60
D62V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                170
  CLUS_2                1                 43
  CLUS_3                3                179

Clustering(63) Variable = 14q loss mutation analysis
D63V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               31                 32
  CLUS_2                2                 30
  CLUS_3                1                 29
  CLUS_4                9                 14
D63V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 43
  CLUS_2               17                 31
  CLUS_3                5                  8
  CLUS_4               20                 23
D63V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               78                 92
  CLUS_2                8                179
  CLUS_3                8                 24
  CLUS_4                0                 24
D63V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               36                 69
  CLUS_2                6                 80
  CLUS_3                6                 57
D63V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               14                 50
  CLUS_2               40                 77
  CLUS_3                0                  7
  CLUS_4                7                 69
D63V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               42                100
  CLUS_2                3                 20
  CLUS_3                3                 45
  CLUS_4               13                 38
D63V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               34                 33
  CLUS_2                4                 54
  CLUS_3                7                 32
  CLUS_4                7                 13
D63V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                6                 58
  CLUS_2                2                 16
  CLUS_3               44                 58
D63V9, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               44                130
  CLUS_2               33                130
  CLUS_3               13                 48
D63V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               45                127
  CLUS_2                6                 38
  CLUS_3               39                143

Clustering(64) Variable = 15q loss mutation analysis
D64V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               26                 37
  CLUS_2                6                 26
  CLUS_3                3                 27
  CLUS_4                7                 16
D64V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                 39
  CLUS_2               16                 32
  CLUS_3                3                 10
  CLUS_4               18                 25
D64V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               70                100
  CLUS_2                9                178
  CLUS_3               19                 13
  CLUS_4                1                 23
D64V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               34                 71
  CLUS_2               12                 74
  CLUS_3               10                 53
D64V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               20                 44
  CLUS_2               25                 92
  CLUS_3                4                  3
  CLUS_4               14                 62
D64V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               36                106
  CLUS_2                5                 18
  CLUS_3                8                 40
  CLUS_4               14                 37
D64V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               27                 40
  CLUS_2               10                 48
  CLUS_3               12                 27
  CLUS_4                6                 14
D64V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                 56
  CLUS_2                7                 11
  CLUS_3               40                 62
D64V9, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               46                128
  CLUS_2               34                129
  CLUS_3               14                 47
D64V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               49                123
  CLUS_2                5                 39
  CLUS_3               40                142

Clustering(65) Variable = 16p loss mutation analysis
D65V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 59
  CLUS_2                0                 32
  CLUS_3                0                 30
  CLUS_4                0                 23
D65V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                2                 46
  CLUS_3                0                 13
  CLUS_4                2                 41
D65V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                6                164
  CLUS_2                2                185
  CLUS_3                1                 31
  CLUS_4                0                 24
D65V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                5                100
  CLUS_2                0                 86
  CLUS_3                0                 63
D65V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                116
  CLUS_3                0                  7
  CLUS_4                1                 75
D65V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                140
  CLUS_2                0                 23
  CLUS_3                1                 47
  CLUS_4                1                 50
D65V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                 64
  CLUS_2                0                 58
  CLUS_3                1                 38
  CLUS_4                0                 20
D65V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 64
  CLUS_2                0                 18
  CLUS_3                4                 98
D65V9, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                170
  CLUS_2                4                159
  CLUS_3                0                 61
D65V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                169
  CLUS_2                1                 43
  CLUS_3                4                178

Clustering(66) Variable = 16q loss mutation analysis
D66V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 59
  CLUS_2                1                 31
  CLUS_3                0                 30
  CLUS_4                0                 23
D66V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 43
  CLUS_2                2                 46
  CLUS_3                0                 13
  CLUS_4                2                 41
D66V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                167
  CLUS_2                2                185
  CLUS_3                2                 30
  CLUS_4                0                 24
D66V4, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                252 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2675 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2679         TCGA-A6-2680         TCGA-A6-2681 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2682         TCGA-A6-2684         TCGA-A6-2685 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2686         TCGA-A6-4105         TCGA-A6-4107 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5667         TCGA-A6-6137         TCGA-A6-6138 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6140         TCGA-A6-6141         TCGA-A6-6142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6649         TCGA-A6-6650 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3488         TCGA-AA-3489 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3492         TCGA-AA-3495         TCGA-AA-3496 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3502         TCGA-AA-3506         TCGA-AA-3510 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3655         TCGA-AA-3660 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3662         TCGA-AA-3663         TCGA-AA-3697 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AD-5900 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6895         TCGA-AD-6899 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AD-6901         TCGA-AD-6963         TCGA-AD-6964 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AD-6965         TCGA-AM-5820         TCGA-AM-5821 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-5543 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4308         TCGA-AZ-4313         TCGA-AZ-4315 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4614         TCGA-AZ-4615 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4684         TCGA-AZ-5403         TCGA-AZ-5407 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5256 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-5796         TCGA-CA-5797         TCGA-CA-6715 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-6716         TCGA-CA-6717         TCGA-CA-6718 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4947         TCGA-CK-4948 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4951         TCGA-CK-4952 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4748         TCGA-CM-4750         TCGA-CM-4751 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6530         TCGA-D5-6531         TCGA-D5-6532 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0X9         TCGA-DM-A0XD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A0XF         TCGA-DM-A1D0         TCGA-DM-A1D4 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A1D6         TCGA-DM-A1D7         TCGA-DM-A1D8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1DB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A1HA         TCGA-DM-A1HB         TCGA-DM-A280 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A288 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A28A         TCGA-DM-A28C         TCGA-DM-A28E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A28F         TCGA-DM-A28G         TCGA-DM-A28H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DM-A28K         TCGA-DM-A28M         TCGA-F4-6459 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6461         TCGA-F4-6463 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6569         TCGA-F4-6570         TCGA-F4-6703 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6704         TCGA-F4-6805         TCGA-F4-6806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6807         TCGA-F4-6808         TCGA-F4-6809 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6854         TCGA-F4-6855         TCGA-F4-6856 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6293         TCGA-G4-6294         TCGA-G4-6295 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6297         TCGA-G4-6298         TCGA-G4-6299 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6302         TCGA-G4-6303         TCGA-G4-6304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6311         TCGA-G4-6314 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6320 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6322         TCGA-G4-6323 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6586         TCGA-G4-6588         TCGA-G4-6625 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6626         TCGA-G4-6627         TCGA-G4-6628 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D66V5, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                262 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2676 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2677         TCGA-A6-2678         TCGA-A6-2680 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2683         TCGA-A6-2684 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2685         TCGA-A6-2686         TCGA-A6-3810 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5667         TCGA-A6-6137         TCGA-A6-6138 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6140         TCGA-A6-6141         TCGA-A6-6142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6649         TCGA-A6-6650 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3510         TCGA-AA-3511         TCGA-AA-3514 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3519         TCGA-AA-3520 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3525 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3548 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3558         TCGA-AA-3560 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3672         TCGA-AA-3678 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3688         TCGA-AA-3695 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3831 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3841         TCGA-AA-3844 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3848         TCGA-AA-3850 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3856 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3869 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3930         TCGA-AA-3947 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3955         TCGA-AA-3968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3982         TCGA-AA-3986 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3989         TCGA-AD-5900         TCGA-AD-6548 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6899         TCGA-AD-6965 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AM-5820         TCGA-AM-5821         TCGA-AU-6004 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4308         TCGA-AZ-4315 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4614         TCGA-AZ-4615 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-4684 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6603 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CA-5254         TCGA-CA-5255 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-5256         TCGA-CA-5796         TCGA-CA-5797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-5914 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4748         TCGA-CM-4750         TCGA-CM-4752 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5538 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6530         TCGA-D5-6531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6461 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6463         TCGA-F4-6569         TCGA-F4-6570 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6294 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6295         TCGA-G4-6297         TCGA-G4-6298 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6302         TCGA-G4-6303 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6306         TCGA-G4-6307 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6309         TCGA-G4-6310         TCGA-G4-6311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6314         TCGA-G4-6315         TCGA-G4-6317 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6320         TCGA-G4-6321         TCGA-G4-6322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6627 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6628 
"16Q LOSS WILD-TYPE" 
D66V6, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                262 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2676 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2677         TCGA-A6-2678         TCGA-A6-2680 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2681         TCGA-A6-2683         TCGA-A6-2684 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-2685         TCGA-A6-2686         TCGA-A6-3810 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-5667         TCGA-A6-6137         TCGA-A6-6138 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6140         TCGA-A6-6141         TCGA-A6-6142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6649         TCGA-A6-6650 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3510         TCGA-AA-3511         TCGA-AA-3514 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3519         TCGA-AA-3520 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3525 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3548 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3558         TCGA-AA-3560 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3672         TCGA-AA-3678 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3681         TCGA-AA-3688         TCGA-AA-3695 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3831 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3833         TCGA-AA-3841         TCGA-AA-3844 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3848         TCGA-AA-3850 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3852         TCGA-AA-3854         TCGA-AA-3856 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3869 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3872         TCGA-AA-3930         TCGA-AA-3947 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3955         TCGA-AA-3968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3982         TCGA-AA-3986 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AA-3989         TCGA-AD-5900         TCGA-AD-6548 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AD-6889         TCGA-AD-6899         TCGA-AD-6965 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AM-5820         TCGA-AM-5821         TCGA-AU-6004 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4308         TCGA-AZ-4315 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4614         TCGA-AZ-4615 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-4684 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6603 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CA-5254         TCGA-CA-5255 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-5256         TCGA-CA-5796         TCGA-CA-5797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-5914 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-4748         TCGA-CM-4750         TCGA-CM-4752 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5538 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6530         TCGA-D5-6531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6461 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6463         TCGA-F4-6569         TCGA-F4-6570 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6294 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6295         TCGA-G4-6297         TCGA-G4-6298 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6302         TCGA-G4-6303 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6304         TCGA-G4-6306         TCGA-G4-6307 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6309         TCGA-G4-6310         TCGA-G4-6311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6314         TCGA-G4-6315         TCGA-G4-6317 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6320         TCGA-G4-6321         TCGA-G4-6322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6627 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G4-6628 
"16Q LOSS WILD-TYPE" 
D66V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                1                 57
  CLUS_3                1                 38
  CLUS_4                0                 20
D66V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 18
  CLUS_3                5                 97
D66V9, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                169
  CLUS_2                1                162
  CLUS_3                0                 61
D66V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                167
  CLUS_2                0                 44
  CLUS_3                1                181

Clustering(67) Variable = 17p loss mutation analysis
D67V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               40                 23
  CLUS_2                7                 25
  CLUS_3                5                 25
  CLUS_4               13                 10
D67V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 37
  CLUS_2               28                 20
  CLUS_3                6                  7
  CLUS_4               24                 19
D67V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1              109                 61
  CLUS_2               26                161
  CLUS_3               16                 16
  CLUS_4               13                 11
D67V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               61                 44
  CLUS_2               19                 67
  CLUS_3               17                 46
D67V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               23                 41
  CLUS_2               52                 65
  CLUS_3                5                  2
  CLUS_4               21                 55
D67V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               61                 81
  CLUS_2                6                 17
  CLUS_3               11                 37
  CLUS_4               23                 28
D67V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               38                 29
  CLUS_2               16                 42
  CLUS_3               13                 26
  CLUS_4               14                  6
D67V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               15                 49
  CLUS_2                7                 11
  CLUS_3               59                 43
D67V9, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               76                 98
  CLUS_2               67                 96
  CLUS_3               18                 43
D67V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               77                 95
  CLUS_2               22                 22
  CLUS_3               62                120

Clustering(68) Variable = 17q loss mutation analysis
D68V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               12                 51
  CLUS_2                2                 30
  CLUS_3                1                 29
  CLUS_4                2                 21
D68V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 41
  CLUS_2               10                 38
  CLUS_3                1                 12
  CLUS_4                3                 40
D68V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               19                151
  CLUS_2                6                181
  CLUS_3                6                 26
  CLUS_4                1                 23
D68V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                7                 98
  CLUS_2                2                 84
  CLUS_3                5                 58
D68V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2                4                113
  CLUS_3                0                  7
  CLUS_4                2                 74
D68V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                6                136
  CLUS_2                1                 22
  CLUS_3                0                 48
  CLUS_4                3                 48
D68V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                 59
  CLUS_2                6                 52
  CLUS_3                4                 35
  CLUS_4                1                 19
D68V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                 56
  CLUS_2                3                 15
  CLUS_3                8                 94
D68V9, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               16                158
  CLUS_2               12                151
  CLUS_3                2                 59
D68V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               17                155
  CLUS_2                3                 41
  CLUS_3               10                172

Clustering(69) Variable = 18p loss mutation analysis
D69V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               53                 10
  CLUS_2                5                 27
  CLUS_3                5                 25
  CLUS_4               16                  7
D69V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 38
  CLUS_2               31                 17
  CLUS_3                8                  5
  CLUS_4               34                  9
D69V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1              143                 27
  CLUS_2               26                161
  CLUS_3               27                  5
  CLUS_4               13                 11
D69V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               81                 24
  CLUS_2               24                 62
  CLUS_3               21                 42
D69V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               31                 33
  CLUS_2               71                 46
  CLUS_3                4                  3
  CLUS_4               24                 52
D69V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               85                 57
  CLUS_2                7                 16
  CLUS_3               12                 36
  CLUS_4               26                 25
D69V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               57                 10
  CLUS_2               13                 45
  CLUS_3               16                 23
  CLUS_4               15                  5
D69V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                 52
  CLUS_2                9                  9
  CLUS_3               80                 22
D69V9, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               90                 84
  CLUS_2               87                 76
  CLUS_3               25                 36
D69V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               93                 79
  CLUS_2               22                 22
  CLUS_3               87                 95

Clustering(70) Variable = 18q loss mutation analysis
D70V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               54                  9
  CLUS_2                6                 26
  CLUS_3                6                 24
  CLUS_4               16                  7
D70V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                7                 37
  CLUS_2               32                 16
  CLUS_3                9                  4
  CLUS_4               34                  9
D70V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1              149                 21
  CLUS_2               33                154
  CLUS_3               27                  5
  CLUS_4               16                  8
D70V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               88                 17
  CLUS_2               28                 58
  CLUS_3               22                 41
D70V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               34                 30
  CLUS_2               72                 45
  CLUS_3                5                  2
  CLUS_4               29                 47
D70V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               88                 54
  CLUS_2                8                 15
  CLUS_3               15                 33
  CLUS_4               29                 22
D70V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               57                 10
  CLUS_2               15                 43
  CLUS_3               18                 21
  CLUS_4               16                  4
D70V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                 52
  CLUS_2               11                  7
  CLUS_3               83                 19
D70V9, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               98                 76
  CLUS_2               95                 68
  CLUS_3               25                 36
D70V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1              100                 72
  CLUS_2               23                 21
  CLUS_3               95                 87

Clustering(71) Variable = 19p loss mutation analysis
D71V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 60
  CLUS_2                1                 31
  CLUS_3                1                 29
  CLUS_4                1                 22
D71V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                3                 45
  CLUS_3                0                 13
  CLUS_4                3                 40
D71V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                7                163
  CLUS_2                2                185
  CLUS_3                5                 27
  CLUS_4                0                 24
D71V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                101
  CLUS_2                0                 86
  CLUS_3                3                 60
D71V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                116
  CLUS_3                1                  6
  CLUS_4                2                 74
D71V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                141
  CLUS_2                1                 22
  CLUS_3                2                 46
  CLUS_4                2                 49
D71V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                2                 56
  CLUS_3                0                 39
  CLUS_4                1                 19
D71V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 18
  CLUS_3                6                 96
D71V9, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                169
  CLUS_2                7                156
  CLUS_3                1                 60
D71V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                167
  CLUS_2                4                 40
  CLUS_3                4                178

Clustering(72) Variable = 19q loss mutation analysis
D72V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 60
  CLUS_2                1                 31
  CLUS_3                1                 29
  CLUS_4                0                 23
D72V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                3                 45
  CLUS_3                0                 13
  CLUS_4                2                 41
D72V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                7                163
  CLUS_2                2                185
  CLUS_3                4                 28
  CLUS_4                0                 24
D72V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                101
  CLUS_2                0                 86
  CLUS_3                3                 60
D72V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 62
  CLUS_2                1                116
  CLUS_3                0                  7
  CLUS_4                2                 74
D72V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                141
  CLUS_2                0                 23
  CLUS_3                2                 46
  CLUS_4                2                 49
D72V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                 63
  CLUS_2                2                 56
  CLUS_3                0                 39
  CLUS_4                0                 20
D72V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                0                 18
  CLUS_3                5                 97
D72V9, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                170
  CLUS_2                7                156
  CLUS_3                1                 60
D72V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                168
  CLUS_2                4                 40
  CLUS_3                4                178

Clustering(73) Variable = 20p loss mutation analysis
D73V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               11                 52
  CLUS_2                0                 32
  CLUS_3                1                 29
  CLUS_4                1                 22
D73V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 44
  CLUS_2                5                 43
  CLUS_3                0                 13
  CLUS_4                8                 35
D73V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               27                143
  CLUS_2                2                185
  CLUS_3                0                 32
  CLUS_4                4                 20
D73V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               13                 92
  CLUS_2                3                 83
  CLUS_3                3                 60
D73V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 60
  CLUS_2               12                105
  CLUS_3                0                  7
  CLUS_4                5                 71
D73V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               14                128
  CLUS_2                2                 21
  CLUS_3                2                 46
  CLUS_4                3                 48
D73V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               10                 57
  CLUS_2                2                 56
  CLUS_3                1                 38
  CLUS_4                1                 19
D73V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 63
  CLUS_2                2                 16
  CLUS_3               11                 91
D73V9, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               13                161
  CLUS_2               14                149
  CLUS_3                4                 57
D73V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               12                160
  CLUS_2                2                 42
  CLUS_3               17                165

Clustering(74) Variable = 21q loss mutation analysis
D74V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               19                 44
  CLUS_2                3                 29
  CLUS_3                2                 28
  CLUS_4                2                 21
D74V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2               15                 33
  CLUS_3                2                 11
  CLUS_4                7                 36
D74V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               40                130
  CLUS_2               15                172
  CLUS_3               13                 19
  CLUS_4                3                 21
D74V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               23                 82
  CLUS_2               13                 73
  CLUS_3                8                 55
D74V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                 53
  CLUS_2               27                 90
  CLUS_3                1                  6
  CLUS_4               12                 64
D74V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               30                112
  CLUS_2                4                 19
  CLUS_3                7                 41
  CLUS_4               10                 41
D74V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               18                 49
  CLUS_2                8                 50
  CLUS_3                4                 35
  CLUS_4                2                 18
D74V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 59
  CLUS_2                5                 13
  CLUS_3               22                 80
D74V9, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               28                146
  CLUS_2               34                129
  CLUS_3                5                 56
D74V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               29                143
  CLUS_2                5                 39
  CLUS_3               33                149

Clustering(75) Variable = 22q loss mutation analysis
D75V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               25                 38
  CLUS_2                2                 30
  CLUS_3                3                 27
  CLUS_4                6                 17
D75V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 42
  CLUS_2               17                 31
  CLUS_3                5                  8
  CLUS_4               12                 31
D75V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               56                114
  CLUS_2               11                176
  CLUS_3               12                 20
  CLUS_4                2                 22
D75V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               24                 81
  CLUS_2               10                 76
  CLUS_3                8                 55
D75V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                 53
  CLUS_2               25                 92
  CLUS_3                4                  3
  CLUS_4               11                 65
D75V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               35                107
  CLUS_2                6                 17
  CLUS_3                3                 45
  CLUS_4                7                 44
D75V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               23                 44
  CLUS_2                8                 50
  CLUS_3                9                 30
  CLUS_4                5                 15
D75V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 58
  CLUS_2                6                 12
  CLUS_3               33                 69
D75V9, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               38                136
  CLUS_2               30                133
  CLUS_3               10                 51
D75V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               41                131
  CLUS_2                5                 39
  CLUS_3               32                150

Clustering(76) Variable = Xq loss mutation analysis
D76V1, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               146 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-3810        TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3675        TCGA-AA-3678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3715 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3818 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3841        TCGA-AA-3842        TCGA-AA-3844 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3864        TCGA-AA-3866 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3977        TCGA-AA-3979        TCGA-AA-3982 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01C        TCGA-AA-A01D        TCGA-AA-A01F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02E        TCGA-AA-A02F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02R        TCGA-AA-A02W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D76V2, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               146 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-3810        TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3675        TCGA-AA-3678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3710        TCGA-AA-3715 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3818 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3841        TCGA-AA-3842        TCGA-AA-3844 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3864        TCGA-AA-3866 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3977        TCGA-AA-3979        TCGA-AA-3982 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01C        TCGA-AA-A01D        TCGA-AA-A01F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02E        TCGA-AA-A02F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02R        TCGA-AA-A02W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D76V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               167
  CLUS_2               2               185
  CLUS_3               0                32
  CLUS_4               0                24
D76V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1               104
  CLUS_2               1                85
  CLUS_3               1                62
D76V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                64
  CLUS_2               3               114
  CLUS_3               0                 7
  CLUS_4               0                76
D76V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               139
  CLUS_2               0                23
  CLUS_3               0                48
  CLUS_4               0                51
D76V7, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               182 
       TCGA-A6-2670        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2679 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2683 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-3807        TCGA-A6-3810 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-4107        TCGA-AA-3488        TCGA-AA-3492        TCGA-AA-3494 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3495        TCGA-AA-3502        TCGA-AA-3506        TCGA-AA-3514 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3524 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3525        TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3531        TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3542        TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3688 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3982        TCGA-AA-3984        TCGA-AA-3986 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A02E        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02R        TCGA-AA-A02W        TCGA-AA-A03F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071        TCGA-AZ-4308 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AZ-4313        TCGA-AZ-4315        TCGA-AZ-4614        TCGA-AZ-4615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4684        TCGA-CA-5256        TCGA-CK-4951 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D76V8, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2               182 
       TCGA-A6-2670        TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2676        TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2679 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2680        TCGA-A6-2681        TCGA-A6-2682        TCGA-A6-2683 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-2684        TCGA-A6-2685        TCGA-A6-3807        TCGA-A6-3810 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A6-4107        TCGA-AA-3488        TCGA-AA-3492        TCGA-AA-3494 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3495        TCGA-AA-3502        TCGA-AA-3506        TCGA-AA-3514 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518        TCGA-AA-3519 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522        TCGA-AA-3524 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3525        TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3531        TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3542        TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3549        TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3556        TCGA-AA-3560        TCGA-AA-3561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3688 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3841 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3982        TCGA-AA-3984        TCGA-AA-3986 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A02E        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02R        TCGA-AA-A02W        TCGA-AA-A03F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071        TCGA-AZ-4308 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AZ-4313        TCGA-AZ-4315        TCGA-AZ-4614        TCGA-AZ-4615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4684        TCGA-CA-5256        TCGA-CK-4951 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4748        TCGA-CM-4750 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D76V9, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3               171
  CLUS_2               2               161
  CLUS_3               0                61
D76V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2               170
  CLUS_2               2                42
  CLUS_3               1               181
                     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")
