
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/6462243/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/6462233/UCEC-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=UCEC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=UCEC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/6462233/UCEC-TP.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/6462243/transformed.cor.cli.txt"

nPatients in clinical file=525, in cluster file=514, common to both=514
[1]  80 514
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               43               471 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               43               471 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              173               341 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              173               341 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               88               426 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               88               426 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               443 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               443 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               42               472 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               42               472 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               76               438 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               76               438 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               502 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               502 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               506 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               506 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               465 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               49               465 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               495 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               495 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74               440 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               74               440 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               60               454 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               60               454 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               63               451 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               63               451 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               61               453 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               61               453 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              114               400 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              114               400 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              150               364 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              150               364 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               20               494 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               20               494 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               505 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               505 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               112                402 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               112                402 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               104                410 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               104                410 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                492 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                492 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                19                495 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                19                495 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                65                449 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                65                449 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                50                464 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                50                464 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                486 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                28                486 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                478 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                478 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                504 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                504 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                491 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                491 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                504 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                504 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                502 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                502 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                28                486 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                28                486 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                65                449 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                65                449 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                474 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                40                474 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                50                464 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                50                464 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                459 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                55                459 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               106                408 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               106                408 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               123                391 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               123                391 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                36                478 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                36                478 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                483 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                483 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               61               453 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               61               453 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               24               490 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               24               490 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               15               499 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               15               499 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               504 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               504 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               498 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               498 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               49               465 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               49               465 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               29               485 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               29               485 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               98               416 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               98               416 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               97               417 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               97               417 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               460 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               54               460 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               72               442 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               72               442 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               498 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               498 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               23               491 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               23               491 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               42               472 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               42               472 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               40               474 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               40               474 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               74               440 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               74               440 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               490 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               490 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100               414 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100               414 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               397 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              117               397 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                474 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                474 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                38                476 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                38                476 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                71                443 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                71                443 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                68                446 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                68                446 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                42                472 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                42                472 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                479 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                35                479 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                86                428 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                86                428 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                455 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                455 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               102                412 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               102                412 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                93                421 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                93                421 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               134                380 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               134                380 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               120                394 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               120                394 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                86                428 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                86                428 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                462 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                462 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                65                449 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                65                449 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                457 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                457 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                52                462 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                52                462 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                496 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                496 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                504 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                504 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                51                463 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                51                463 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               105                409 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               105                409 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               445 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               69               445 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 514 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 514 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=6, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        2      2      0      0
  1P GAIN WILD-TYPE     12     15     12     10
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                15
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        2      0      2
  1P GAIN WILD-TYPE     17     19     13
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               0                19
  CLUS_3               2                13
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P GAIN MUTATED        6      3     32      1      1      0
  1P GAIN WILD-TYPE    294     21    120     21     14      1
D1V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       25      5      8
  1P GAIN WILD-TYPE    127     83    152
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              25               127
  CLUS_2               5                83
  CLUS_3               8               152
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P GAIN MUTATED        2      6      0      1      1      2
  1P GAIN WILD-TYPE     39     31     39     11     40     22
D1V5, multiclass
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5   7
  1P GAIN WILD-TYPE 116  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    7
  1P GAIN WILD-TYPE  116   66
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5               116
  CLUS_2               7                66
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED       29      5      4      5
  1P GAIN WILD-TYPE    145     81    111    125
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              29               145
  CLUS_2               5                81
  CLUS_3               4               111
  CLUS_4               5               125
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       32      4      7
  1P GAIN WILD-TYPE    207     80    175
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              32               207
  CLUS_2               4                80
  CLUS_3               7               175
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P GAIN MUTATED       27      2      2      5      6
  1P GAIN WILD-TYPE    122    136     47     48    110
D1V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        0      5     37
  1P GAIN WILD-TYPE     13    209    241
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               5               209
  CLUS_3              37               241
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED       29      3      5
  1P GAIN WILD-TYPE    147     87    111
D1V11, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1              29               147
  CLUS_2               3                87
  CLUS_3               5               111
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        8     19      7      3
  1P GAIN WILD-TYPE     93     81    139     32
D1V12, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               8                93
  CLUS_2              19                81
  CLUS_3               7               139
  CLUS_4               3                32

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED        9      6      5      2
  1Q GAIN WILD-TYPE      5     11      7      8
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9                 5
  CLUS_2               6                11
  CLUS_3               5                 7
  CLUS_4               2                 8
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       11      6      5
  1Q GAIN WILD-TYPE      8     13     10
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              11                 8
  CLUS_2               6                13
  CLUS_3               5                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q GAIN MUTATED       90     15     48     10      9      1
  1Q GAIN WILD-TYPE    210      9    104     12      6      0
D2V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       49     20     55
  1Q GAIN WILD-TYPE    103     68    105
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              49               103
  CLUS_2              20                68
  CLUS_3              55               105
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q GAIN MUTATED       10     10     16      8     17      8
  1Q GAIN WILD-TYPE     31     27     23      4     24     16
D2V5, multiclass
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   51 18
  1Q GAIN WILD-TYPE 70 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     51   18
  1Q GAIN WILD-TYPE   70   55
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              51                70
  CLUS_2              18                55
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED       57     35     46     32
  1Q GAIN WILD-TYPE    117     51     69     98
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              57               117
  CLUS_2              35                51
  CLUS_3              46                69
  CLUS_4              32                98
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       75     38     57
  1Q GAIN WILD-TYPE    164     46    125
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              75               164
  CLUS_2              38                46
  CLUS_3              57               125
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q GAIN MUTATED       49     37     16     28     42
  1Q GAIN WILD-TYPE    100    101     33     25     74
D2V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED        2     70    100
  1Q GAIN WILD-TYPE     11    144    178
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2              70               144
  CLUS_3             100               178
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q GAIN MUTATED       56     31     36
  1Q GAIN WILD-TYPE    120     59     80
D2V11, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              56               120
  CLUS_2              31                59
  CLUS_3              36                80
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q GAIN MUTATED       35     38     45      5
  1Q GAIN WILD-TYPE     66     62    101     30
D2V12, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              35                66
  CLUS_2              38                62
  CLUS_3              45               101
  CLUS_4               5                30

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED        1      3      2      1
  2P GAIN WILD-TYPE     13     14     10      9
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               1                 9
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        2      2      3
  2P GAIN WILD-TYPE     17     17     12
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               2                17
  CLUS_3               3                12
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2P GAIN MUTATED        8     21     52      2      5      0
  2P GAIN WILD-TYPE    292      3    100     20     10      1
D3V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       47     10     10
  2P GAIN WILD-TYPE    105     78    150
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              47               105
  CLUS_2              10                78
  CLUS_3              10               150
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2P GAIN MUTATED        4      7      1      1      6      7
  2P GAIN WILD-TYPE     37     30     38     11     35     17
D3V5, multiclass
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    16  10
  2P GAIN WILD-TYPE 105  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     16   10
  2P GAIN WILD-TYPE  105   63
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              16               105
  CLUS_2              10                63
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED       53     11     13      9
  2P GAIN WILD-TYPE    121     75    102    121
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              53               121
  CLUS_2              11                75
  CLUS_3              13               102
  CLUS_4               9               121
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       64      8     14
  2P GAIN WILD-TYPE    175     76    168
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              64               175
  CLUS_2               8                76
  CLUS_3              14               168
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P GAIN MUTATED       43      9     13      9     13
  2P GAIN WILD-TYPE    106    129     36     44    103
D3V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED        0     18     69
  2P GAIN WILD-TYPE     13    196    209
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2              18               196
  CLUS_3              69               209
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P GAIN MUTATED       40     18      7
  2P GAIN WILD-TYPE    136     72    109
D3V11, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              40               136
  CLUS_2              18                72
  CLUS_3               7               109
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P GAIN MUTATED       23     28     10      4
  2P GAIN WILD-TYPE     78     72    136     31
D3V12, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              23                78
  CLUS_2              28                72
  CLUS_3              10               136
  CLUS_4               4                31

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED        0      1      2      0
  2Q GAIN WILD-TYPE     14     16     10     10
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                16
  CLUS_3               2                10
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        1      1      1
  2Q GAIN WILD-TYPE     18     18     14
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                18
  CLUS_3               1                14
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q GAIN MUTATED        5     19     41      2      4      0
  2Q GAIN WILD-TYPE    295      5    111     20     11      1
D4V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       40      8      9
  2Q GAIN WILD-TYPE    112     80    151
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              40               112
  CLUS_2               8                80
  CLUS_3               9               151
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q GAIN MUTATED        3      5      1      1      4      7
  2Q GAIN WILD-TYPE     38     32     38     11     37     17
D4V5, multiclass
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14   7
  2Q GAIN WILD-TYPE 107  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14    7
  2Q GAIN WILD-TYPE  107   66
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              14               107
  CLUS_2               7                66
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED       42     10     10      7
  2Q GAIN WILD-TYPE    132     76    105    123
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              42               132
  CLUS_2              10                76
  CLUS_3              10               105
  CLUS_4               7               123
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       52      6     11
  2Q GAIN WILD-TYPE    187     78    171
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              52               187
  CLUS_2               6                78
  CLUS_3              11               171
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q GAIN MUTATED       37      7     10      7     10
  2Q GAIN WILD-TYPE    112    131     39     46    106
D4V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED        0     13     58
  2Q GAIN WILD-TYPE     13    201    220
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2              13               201
  CLUS_3              58               220
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q GAIN MUTATED       35     15      5
  2Q GAIN WILD-TYPE    141     75    111
D4V11, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              35               141
  CLUS_2              15                75
  CLUS_3               5               111
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q GAIN MUTATED       20     24      7      4
  2Q GAIN WILD-TYPE     81     76    139     31
D4V12, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1              20                81
  CLUS_2              24                76
  CLUS_3               7               139
  CLUS_4               4                31

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        0      1      1      0
  3P GAIN WILD-TYPE     14     16     11     10
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-BG-A0LW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        1      1      0
  3P GAIN WILD-TYPE     18     18     15
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-BG-A0LW 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P GAIN MUTATED        2      3     24      4      9      0
  3P GAIN WILD-TYPE    298     21    128     18      6      1
D5V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       23      6      7
  3P GAIN WILD-TYPE    129     82    153
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              23               129
  CLUS_2               6                82
  CLUS_3               7               153
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P GAIN MUTATED        3      1      2      1      0      0
  3P GAIN WILD-TYPE     38     36     37     11     41     24
D5V5, multiclass
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5   2
  3P GAIN WILD-TYPE 116  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5    2
  3P GAIN WILD-TYPE  116   71
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5               116
  CLUS_2               2                71
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED       26      6      1      8
  3P GAIN WILD-TYPE    148     80    114    122
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              26               148
  CLUS_2               6                80
  CLUS_3               1               114
  CLUS_4               8               122
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       30      3      8
  3P GAIN WILD-TYPE    209     81    174
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              30               209
  CLUS_2               3                81
  CLUS_3               8               174
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P GAIN MUTATED       19      7      7      2      7
  3P GAIN WILD-TYPE    130    131     42     51    109
D5V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED        3      9     30
  3P GAIN WILD-TYPE     10    205    248
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               9               205
  CLUS_3              30               248
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P GAIN MUTATED       23      6      6
  3P GAIN WILD-TYPE    153     84    110
D5V11, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              23               153
  CLUS_2               6                84
  CLUS_3               6               110
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P GAIN MUTATED        8     17      8      2
  3P GAIN WILD-TYPE     93     83    138     33
D5V12, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               8                93
  CLUS_2              17                83
  CLUS_3               8               138
  CLUS_4               2                33

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED        1      3      1      0
  3Q GAIN WILD-TYPE     13     14     11     10
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               1                11
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        2      1      2
  3Q GAIN WILD-TYPE     17     18     13
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               1                18
  CLUS_3               2                13
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q GAIN MUTATED        5      4     52      5     10      0
  3Q GAIN WILD-TYPE    295     20    100     17      5      1
D6V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       48     10      8
  3Q GAIN WILD-TYPE    104     78    152
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              48               104
  CLUS_2              10                78
  CLUS_3               8               152
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q GAIN MUTATED        6      4      2      1      0      1
  3Q GAIN WILD-TYPE     35     33     37     11     41     23
D6V5, multiclass
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5   9
  3Q GAIN WILD-TYPE 116  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    9
  3Q GAIN WILD-TYPE  116   64
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5               116
  CLUS_2               9                64
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED       52     13      1      9
  3Q GAIN WILD-TYPE    122     73    114    121
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              52               122
  CLUS_2              13                73
  CLUS_3               1               114
  CLUS_4               9               121
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       63      3      9
  3Q GAIN WILD-TYPE    176     81    173
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              63               176
  CLUS_2               3                81
  CLUS_3               9               173
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q GAIN MUTATED       39      9     12      3     13
  3Q GAIN WILD-TYPE    110    129     37     50    103
D6V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED        3     10     63
  3Q GAIN WILD-TYPE     10    204    215
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2              10               204
  CLUS_3              63               215
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q GAIN MUTATED       41     16      7
  3Q GAIN WILD-TYPE    135     74    109
D6V11, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              41               135
  CLUS_2              16                74
  CLUS_3               7               109
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q GAIN MUTATED       19     33      9      3
  3Q GAIN WILD-TYPE     82     67    137     32
D6V12, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              19                82
  CLUS_2              33                67
  CLUS_3               9               137
  CLUS_4               3                32

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        1      0      0      0
  4P GAIN WILD-TYPE     13     17     12     10
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        1      0      0
  4P GAIN WILD-TYPE     18     19     15
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P GAIN MUTATED        0      0     11      1      0      0
  4P GAIN WILD-TYPE    300     24    141     21     15      1
D7V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        4      2      2
  4P GAIN WILD-TYPE    148     86    158
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4               148
  CLUS_2               2                86
  CLUS_3               2               158
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P GAIN MUTATED        2      2      0      0      0      1
  4P GAIN WILD-TYPE     39     35     39     12     41     23
D7V5, multiclass
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   5
  4P GAIN WILD-TYPE 121  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    5
  4P GAIN WILD-TYPE  121   68
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0               121
  CLUS_2               5                68
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED       10      0      1      1
  4P GAIN WILD-TYPE    164     86    114    129
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              10               164
  CLUS_2               0                86
  CLUS_3               1               114
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED       10      0      2
  4P GAIN WILD-TYPE    229     84    180
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1              10               229
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P GAIN MUTATED        6      1      2      0      3
  4P GAIN WILD-TYPE    143    137     47     53    113
D7V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        0      1     11
  4P GAIN WILD-TYPE     13    213    267
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               1               213
  CLUS_3              11               267
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        6      1      1
  4P GAIN WILD-TYPE    170     89    115
D7V11, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               6               170
  CLUS_2               1                89
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        3      2      1      2
  4P GAIN WILD-TYPE     98     98    145     33
D7V12, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                98
  CLUS_2               2                98
  CLUS_3               1               145
  CLUS_4               2                33

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        1      0      0      0
  4Q GAIN WILD-TYPE     13     17     12     10
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        1      0      0
  4Q GAIN WILD-TYPE     18     19     15
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q GAIN MUTATED        0      0      7      1      0      0
  4Q GAIN WILD-TYPE    300     24    145     21     15      1
D8V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        4      1      2
  4Q GAIN WILD-TYPE    148     87    158
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4               148
  CLUS_2               1                87
  CLUS_3               2               158
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q GAIN MUTATED        1      1      0      0      0      0
  4Q GAIN WILD-TYPE     40     36     39     12     41     24
D8V5, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G9        TCGA-A5-A0GA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A13C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   2
  4Q GAIN WILD-TYPE 121  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    2
  4Q GAIN WILD-TYPE  121   71
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        6      0      1      1
  4Q GAIN WILD-TYPE    168     86    114    129
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               6               168
  CLUS_2               0                86
  CLUS_3               1               114
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        6      0      2
  4Q GAIN WILD-TYPE    233     84    180
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               6               233
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        4      1      2      0      1
  4Q GAIN WILD-TYPE    145    137     47     53    115
D8V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        0      1      7
  4Q GAIN WILD-TYPE     13    213    271
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               1               213
  CLUS_3               7               271
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        5      1      1
  4Q GAIN WILD-TYPE    171     89    115
D8V11, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               5               171
  CLUS_2               1                89
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        1      3      1      2
  4Q GAIN WILD-TYPE    100     97    145     33
D8V12, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               100
  CLUS_2               3                97
  CLUS_3               1               145
  CLUS_4               2                33

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED        1      2      1      0
  5P GAIN WILD-TYPE     13     15     11     10
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                15
  CLUS_3               1                11
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        2      0      2
  5P GAIN WILD-TYPE     17     19     13
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               0                19
  CLUS_3               2                13
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P GAIN MUTATED        3      3     40      3      0      0
  5P GAIN WILD-TYPE    297     21    112     19     15      1
D9V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       32      4      5
  5P GAIN WILD-TYPE    120     84    155
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              32               120
  CLUS_2               4                84
  CLUS_3               5               155
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P GAIN MUTATED        1      3      0      0      4      4
  5P GAIN WILD-TYPE     40     34     39     12     37     20
D9V5, multiclass
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     8   4
  5P GAIN WILD-TYPE 113  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8    4
  5P GAIN WILD-TYPE  113   69
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8               113
  CLUS_2               4                69
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED       39      4      6      0
  5P GAIN WILD-TYPE    135     82    109    130
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              39               135
  CLUS_2               4                82
  CLUS_3               6               109
  CLUS_4               0               130
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       42      2      5
  5P GAIN WILD-TYPE    197     82    177
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              42               197
  CLUS_2               2                82
  CLUS_3               5               177
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5P GAIN MUTATED       32      1      4      6      5
  5P GAIN WILD-TYPE    117    137     45     47    111
D9V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED        2      5     41
  5P GAIN WILD-TYPE     11    209    237
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               5               209
  CLUS_3              41               237
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P GAIN MUTATED       30      7      2
  5P GAIN WILD-TYPE    146     83    114
D9V11, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              30               146
  CLUS_2               7                83
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P GAIN MUTATED       10     24      3      2
  5P GAIN WILD-TYPE     91     76    143     33
D9V12, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              10                91
  CLUS_2              24                76
  CLUS_3               3               143
  CLUS_4               2                33

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED        0      0      0      0
  5Q GAIN WILD-TYPE     14     17     12     10
D10V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        0      0      0
  5Q GAIN WILD-TYPE     19     19     15
D10V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q GAIN MUTATED        1      1     14      3      0      0
  5Q GAIN WILD-TYPE    299     23    138     19     15      1
D10V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       12      2      4
  5Q GAIN WILD-TYPE    140     86    156
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              12               140
  CLUS_2               2                86
  CLUS_3               4               156
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q GAIN MUTATED        0      2      0      0      2      0
  5Q GAIN WILD-TYPE     41     35     39     12     39     24
D10V5, multiclass
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3   1
  5Q GAIN WILD-TYPE 118  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    1
  5Q GAIN WILD-TYPE  118   72
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3               118
  CLUS_2               1                72
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED       13      3      3      0
  5Q GAIN WILD-TYPE    161     83    112    130
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              13               161
  CLUS_2               3                83
  CLUS_3               3               112
  CLUS_4               0               130
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       16      1      2
  5Q GAIN WILD-TYPE    223     83    180
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              16               223
  CLUS_2               1                83
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q GAIN MUTATED       10      0      3      4      2
  5Q GAIN WILD-TYPE    139    138     46     49    114
D10V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED        1      2     16
  5Q GAIN WILD-TYPE     12    212    262
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2               212
  CLUS_3              16               262
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q GAIN MUTATED       12      3      1
  5Q GAIN WILD-TYPE    164     87    115
D10V11, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1              12               164
  CLUS_2               3                87
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q GAIN MUTATED        3     11      1      1
  5Q GAIN WILD-TYPE     98     89    145     34
D10V12, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                98
  CLUS_2              11                89
  CLUS_3               1               145
  CLUS_4               1                34

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED        0      3      2      0
  6P GAIN WILD-TYPE     14     14     10     10
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        0      2      3
  6P GAIN WILD-TYPE     19     17     12
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               2                17
  CLUS_3               3                12
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P GAIN MUTATED        5      2     56      2      9      0
  6P GAIN WILD-TYPE    295     22     96     20      6      1
D11V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       43     13     10
  6P GAIN WILD-TYPE    109     75    150
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              43               109
  CLUS_2              13                75
  CLUS_3              10               150
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P GAIN MUTATED        4      6      2      1      0      2
  6P GAIN WILD-TYPE     37     31     37     11     41     22
D11V5, multiclass
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6   9
  6P GAIN WILD-TYPE 115  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    9
  6P GAIN WILD-TYPE  115   64
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               6               115
  CLUS_2               9                64
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED       49      6      5     14
  6P GAIN WILD-TYPE    125     80    110    116
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              49               125
  CLUS_2               6                80
  CLUS_3               5               110
  CLUS_4              14               116
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       57      3     14
  6P GAIN WILD-TYPE    182     81    168
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              57               182
  CLUS_2               3                81
  CLUS_3              14               168
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P GAIN MUTATED       40     11     11      4      8
  6P GAIN WILD-TYPE    109    127     38     49    108
D11V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED        1     13     60
  6P GAIN WILD-TYPE     12    201    218
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2              13               201
  CLUS_3              60               218
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P GAIN MUTATED       40     12     12
  6P GAIN WILD-TYPE    136     78    104
D11V11, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              40               136
  CLUS_2              12                78
  CLUS_3              12               104
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P GAIN MUTATED       18     26     14      6
  6P GAIN WILD-TYPE     83     74    132     29
D11V12, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              18                83
  CLUS_2              26                74
  CLUS_3              14               132
  CLUS_4               6                29

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q GAIN MUTATED        0      3      2      0
  6Q GAIN WILD-TYPE     14     14     10     10
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED        0      2      3
  6Q GAIN WILD-TYPE     19     17     12
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               2                17
  CLUS_3               3                12
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q GAIN MUTATED        5      2     43      2      8      0
  6Q GAIN WILD-TYPE    295     22    109     20      7      1
D12V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       32      9     11
  6Q GAIN WILD-TYPE    120     79    149
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              32               120
  CLUS_2               9                79
  CLUS_3              11               149
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q GAIN MUTATED        4      6      1      1      0      2
  6Q GAIN WILD-TYPE     37     31     38     11     41     22
D12V5, multiclass
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     5   9
  6Q GAIN WILD-TYPE 116  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    9
  6Q GAIN WILD-TYPE  116   64
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5               116
  CLUS_2               9                64
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q GAIN MUTATED       35      6      5     14
  6Q GAIN WILD-TYPE    139     80    110    116
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              35               139
  CLUS_2               6                80
  CLUS_3               5               110
  CLUS_4              14               116
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       43      3     14
  6Q GAIN WILD-TYPE    196     81    168
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              43               196
  CLUS_2               3                81
  CLUS_3              14               168
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6Q GAIN MUTATED       29     11      9      4      7
  6Q GAIN WILD-TYPE    120    127     40     49    109
D12V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED        1     13     46
  6Q GAIN WILD-TYPE     12    201    232
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2              13               201
  CLUS_3              46               232
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q GAIN MUTATED       27     11     12
  6Q GAIN WILD-TYPE    149     79    104
D12V11, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              27               149
  CLUS_2              11                79
  CLUS_3              12               104
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q GAIN MUTATED       14     18     13      5
  6Q GAIN WILD-TYPE     87     82    133     30
D12V12, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              14                87
  CLUS_2              18                82
  CLUS_3              13               133
  CLUS_4               5                30

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED        1      3      2      1
  7P GAIN WILD-TYPE     13     14     10      9
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               1                 9
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        2      3      2
  7P GAIN WILD-TYPE     17     16     13
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                16
  CLUS_3               2                13
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P GAIN MUTATED        8     14     27      7      7      0
  7P GAIN WILD-TYPE    292     10    125     15      8      1
D13V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       26      4     17
  7P GAIN WILD-TYPE    126     84    143
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              26               126
  CLUS_2               4                84
  CLUS_3              17               143
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P GAIN MUTATED        3      5      3      1      5      1
  7P GAIN WILD-TYPE     38     32     36     11     36     23
D13V5, multiclass
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    13   5
  7P GAIN WILD-TYPE 108  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13    5
  7P GAIN WILD-TYPE  108   68
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13               108
  CLUS_2               5                68
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       32      5     12     12
  7P GAIN WILD-TYPE    142     81    103    118
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              32               142
  CLUS_2               5                81
  CLUS_3              12               103
  CLUS_4              12               118
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       36      7     18
  7P GAIN WILD-TYPE    203     77    164
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              36               203
  CLUS_2               7                77
  CLUS_3              18               164
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P GAIN MUTATED       25     10      6      9     12
  7P GAIN WILD-TYPE    124    128     43     44    104
D13V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED        1     17     44
  7P GAIN WILD-TYPE     12    197    234
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2              17               197
  CLUS_3              44               234
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P GAIN MUTATED       26     11     10
  7P GAIN WILD-TYPE    150     79    106
D13V11, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              26               150
  CLUS_2              11                79
  CLUS_3              10               106
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P GAIN MUTATED       10     16     16      5
  7P GAIN WILD-TYPE     91     84    130     30
D13V12, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              10                91
  CLUS_2              16                84
  CLUS_3              16               130
  CLUS_4               5                30

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED        1      3      2      1
  7Q GAIN WILD-TYPE     13     14     10      9
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               2                10
  CLUS_4               1                 9
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        2      3      2
  7Q GAIN WILD-TYPE     17     16     13
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                16
  CLUS_3               2                13
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q GAIN MUTATED       11     15     22      6      7      0
  7Q GAIN WILD-TYPE    289      9    130     16      8      1
D14V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       22      3     20
  7Q GAIN WILD-TYPE    130     85    140
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              22               130
  CLUS_2               3                85
  CLUS_3              20               140
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q GAIN MUTATED        2      3      3      1      5      1
  7Q GAIN WILD-TYPE     39     34     36     11     36     23
D14V5, multiclass
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    12   3
  7Q GAIN WILD-TYPE 109  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12    3
  7Q GAIN WILD-TYPE  109   70
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              12               109
  CLUS_2               3                70
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED       28      5     13     13
  7Q GAIN WILD-TYPE    146     81    102    117
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28               146
  CLUS_2               5                81
  CLUS_3              13               102
  CLUS_4              13               117
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       33      7     19
  7Q GAIN WILD-TYPE    206     77    163
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              33               206
  CLUS_2               7                77
  CLUS_3              19               163
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q GAIN MUTATED       21     12      5     10     13
  7Q GAIN WILD-TYPE    128    126     44     43    103
D14V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED        1     19     41
  7Q GAIN WILD-TYPE     12    195    237
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2              19               195
  CLUS_3              41               237
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q GAIN MUTATED       22     12     11
  7Q GAIN WILD-TYPE    154     78    105
D14V11, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              22               154
  CLUS_2              12                78
  CLUS_3              11               105
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q GAIN MUTATED        9     14     18      4
  7Q GAIN WILD-TYPE     92     86    128     31
D14V12, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               9                92
  CLUS_2              14                86
  CLUS_3              18               128
  CLUS_4               4                31

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        1      4      2      0
  8P GAIN WILD-TYPE     13     13     10     10
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                13
  CLUS_3               2                10
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        1      3      3
  8P GAIN WILD-TYPE     18     16     12
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               3                16
  CLUS_3               3                12
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P GAIN MUTATED       38      6     41     14     15      0
  8P GAIN WILD-TYPE    262     18    111      8      0      1
D15V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       37     20     39
  8P GAIN WILD-TYPE    115     68    121
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              37               115
  CLUS_2              20                68
  CLUS_3              39               121
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P GAIN MUTATED        7     10      4      2      2      8
  8P GAIN WILD-TYPE     34     27     35     10     39     16
D15V5, multiclass
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    20  13
  8P GAIN WILD-TYPE 101  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     20   13
  8P GAIN WILD-TYPE  101   60
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              20               101
  CLUS_2              13                60
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED       47     11     28     26
  8P GAIN WILD-TYPE    127     75     87    104
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              47               127
  CLUS_2              11                75
  CLUS_3              28                87
  CLUS_4              26               104
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       61     14     37
  8P GAIN WILD-TYPE    178     70    145
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              61               178
  CLUS_2              14                70
  CLUS_3              37               145
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P GAIN MUTATED       36     28     11     19     19
  8P GAIN WILD-TYPE    113    110     38     34     97
D15V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        3     41     69
  8P GAIN WILD-TYPE     10    173    209
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2              41               173
  CLUS_3              69               209
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       47     19     27
  8P GAIN WILD-TYPE    129     71     89
D15V11, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              47               129
  CLUS_2              19                71
  CLUS_3              27                89
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED       20     27     34     12
  8P GAIN WILD-TYPE     81     73    112     23
D15V12, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              20                81
  CLUS_2              27                73
  CLUS_3              34               112
  CLUS_4              12                23

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        1      8      2      0
  8Q GAIN WILD-TYPE     13      9     10     10
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               8                 9
  CLUS_3               2                10
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        1      3      7
  8Q GAIN WILD-TYPE     18     16      8
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               3                16
  CLUS_3               7                 8
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q GAIN MUTATED       40      7     72     15     15      1
  8Q GAIN WILD-TYPE    260     17     80      7      0      0
D16V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       55     26     44
  8Q GAIN WILD-TYPE     97     62    116
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              55                97
  CLUS_2              26                62
  CLUS_3              44               116
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q GAIN MUTATED        9     12      7      2      2     13
  8Q GAIN WILD-TYPE     32     25     32     10     39     11
D16V5, multiclass
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   27 18
  8Q GAIN WILD-TYPE 94 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     27   18
  8Q GAIN WILD-TYPE   94   55
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              27                94
  CLUS_2              18                55
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED       72     17     30     29
  8Q GAIN WILD-TYPE    102     69     85    101
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              72               102
  CLUS_2              17                69
  CLUS_3              30                85
  CLUS_4              29               101
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       91     15     42
  8Q GAIN WILD-TYPE    148     69    140
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              91               148
  CLUS_2              15                69
  CLUS_3              42               140
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q GAIN MUTATED       61     33     13     20     20
  8Q GAIN WILD-TYPE     88    105     36     33     96
D16V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        4     46     97
  8Q GAIN WILD-TYPE      9    168    181
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                 9
  CLUS_2              46               168
  CLUS_3              97               181
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       65     25     30
  8Q GAIN WILD-TYPE    111     65     86
D16V11, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              65               111
  CLUS_2              25                65
  CLUS_3              30                86
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED       29     37     39     15
  8Q GAIN WILD-TYPE     72     63    107     20
D16V12, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              29                72
  CLUS_2              37                63
  CLUS_3              39               107
  CLUS_4              15                20

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        1      1      0      0
  9P GAIN WILD-TYPE     13     16     12     10
D17V1, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06F        TCGA-AX-A06J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        1      0      1
  9P GAIN WILD-TYPE     18     19     14
D17V2, multiclass
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06F        TCGA-AX-A06J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P GAIN MUTATED        4      0     15      1      0      0
  9P GAIN WILD-TYPE    296     24    137     21     15      1
D17V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       13      2      3
  9P GAIN WILD-TYPE    139     86    157
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              13               139
  CLUS_2               2                86
  CLUS_3               3               157
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P GAIN MUTATED        3      2      0      0      0      0
  9P GAIN WILD-TYPE     38     35     39     12     41     24
D17V5, multiclass
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2   3
  9P GAIN WILD-TYPE 119  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    3
  9P GAIN WILD-TYPE  119   70
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2               119
  CLUS_2               3                70
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED       11      4      4      1
  9P GAIN WILD-TYPE    163     82    111    129
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              11               163
  CLUS_2               4                82
  CLUS_3               4               111
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       16      2      2
  9P GAIN WILD-TYPE    223     82    180
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              16               223
  CLUS_2               2                82
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P GAIN MUTATED       14      2      0      2      2
  9P GAIN WILD-TYPE    135    136     49     51    114
D17V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED        0      4     16
  9P GAIN WILD-TYPE     13    210    262
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               4               210
  CLUS_3              16               262
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P GAIN MUTATED       10      4      2
  9P GAIN WILD-TYPE    166     86    114
D17V11, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              10               166
  CLUS_2               4                86
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P GAIN MUTATED        5      6      3      2
  9P GAIN WILD-TYPE     96     94    143     33
D17V12, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               5                96
  CLUS_2               6                94
  CLUS_3               3               143
  CLUS_4               2                33

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        0      0      0      0
  9Q GAIN WILD-TYPE     14     17     12     10
D18V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        0      0      0
  9Q GAIN WILD-TYPE     19     19     15
D18V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q GAIN MUTATED        2      0      6      1      0      0
  9Q GAIN WILD-TYPE    298     24    146     21     15      1
D18V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        6      0      3
  9Q GAIN WILD-TYPE    146     88    157
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6               146
  CLUS_2               0                88
  CLUS_3               3               157
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q GAIN MUTATED        1      1      0      0      0      0
  9Q GAIN WILD-TYPE     40     36     39     12     41     24
D18V5, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0   2
  9Q GAIN WILD-TYPE 121  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    2
  9Q GAIN WILD-TYPE  121   71
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        5      2      1      1
  9Q GAIN WILD-TYPE    169     84    114    129
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               5               169
  CLUS_2               2                84
  CLUS_3               1               114
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        7      1      1
  9Q GAIN WILD-TYPE    232     83    181
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               7               232
  CLUS_2               1                83
  CLUS_3               1               181
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q GAIN MUTATED        7      1      0      1      0
  9Q GAIN WILD-TYPE    142    137     49     52    116
D18V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        0      1      8
  9Q GAIN WILD-TYPE     13    213    270
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                13
  CLUS_2               1               213
  CLUS_3               8               270
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q GAIN MUTATED        6      1      1
  9Q GAIN WILD-TYPE    170     89    115
D18V11, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6               170
  CLUS_2               1                89
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q GAIN MUTATED        1      3      2      2
  9Q GAIN WILD-TYPE    100     97    144     33
D18V12, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1               100
  CLUS_2               3                97
  CLUS_3               2               144
  CLUS_4               2                33

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED        2      2      8      2
  10P GAIN WILD-TYPE     12     15      4      8
D19V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                 15
  CLUS_3                8                  4
  CLUS_4                2                  8
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        3      9      2
  10P GAIN WILD-TYPE     16     10     13
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                9                 10
  CLUS_3                2                 13
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P GAIN MUTATED       47     14     37      7      7      0
  10P GAIN WILD-TYPE    253     10    115     15      8      1
D19V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       32     16     36
  10P GAIN WILD-TYPE    120     72    124
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               32                120
  CLUS_2               16                 72
  CLUS_3               36                124
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P GAIN MUTATED        7      5      8      3     13      9
  10P GAIN WILD-TYPE     34     32     31      9     28     15
D19V5, multiclass
D19V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   32 13
  10P GAIN WILD-TYPE 89 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     32   13
  10P GAIN WILD-TYPE   89   60
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               32                 89
  CLUS_2               13                 60
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED       38     13     24     34
  10P GAIN WILD-TYPE    136     73     91     96
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               38                136
  CLUS_2               13                 73
  CLUS_3               24                 91
  CLUS_4               34                 96
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       49     10     50
  10P GAIN WILD-TYPE    190     74    132
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               49                190
  CLUS_2               10                 74
  CLUS_3               50                132
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P GAIN MUTATED       33     36     13     10     20
  10P GAIN WILD-TYPE    116    102     36     43     96
D19V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED        2     54     56
  10P GAIN WILD-TYPE     11    160    222
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2               54                160
  CLUS_3               56                222
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P GAIN MUTATED       36     13     30
  10P GAIN WILD-TYPE    140     77     86
D19V11, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               36                140
  CLUS_2               13                 77
  CLUS_3               30                 86
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P GAIN MUTATED       16     21     35      7
  10P GAIN WILD-TYPE     85     79    111     28
D19V12, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               16                 85
  CLUS_2               21                 79
  CLUS_3               35                111
  CLUS_4                7                 28

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        1      3      8      2
  10Q GAIN WILD-TYPE     13     14      4      8
D20V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                 14
  CLUS_3                8                  4
  CLUS_4                2                  8
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        2      9      3
  10Q GAIN WILD-TYPE     17     10     12
D20V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                9                 10
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q GAIN MUTATED       46     16     31      5      6      0
  10Q GAIN WILD-TYPE    254      8    121     17      9      1
D20V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       28     15     34
  10Q GAIN WILD-TYPE    124     73    126
D20V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               28                124
  CLUS_2               15                 73
  CLUS_3               34                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q GAIN MUTATED        7      4      8      2     14      8
  10Q GAIN WILD-TYPE     34     33     31     10     27     16
D20V5, multiclass
D20V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   31 12
  10Q GAIN WILD-TYPE 90 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     31   12
  10Q GAIN WILD-TYPE   90   61
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               31                 90
  CLUS_2               12                 61
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED       34     10     24     33
  10Q GAIN WILD-TYPE    140     76     91     97
D20V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               34                140
  CLUS_2               10                 76
  CLUS_3               24                 91
  CLUS_4               33                 97
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       43     11     47
  10Q GAIN WILD-TYPE    196     73    135
D20V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               43                196
  CLUS_2               11                 73
  CLUS_3               47                135
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q GAIN MUTATED       29     35     12     10     18
  10Q GAIN WILD-TYPE    120    103     37     43     98
D20V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        2     53     49
  10Q GAIN WILD-TYPE     11    161    229
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2               53                161
  CLUS_3               49                229
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED       32     12     28
  10Q GAIN WILD-TYPE    144     78     88
D20V11, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               32                144
  CLUS_2               12                 78
  CLUS_3               28                 88
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED       13     21     32      6
  10Q GAIN WILD-TYPE     88     79    114     29
D20V12, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1               13                 88
  CLUS_2               21                 79
  CLUS_3               32                114
  CLUS_4                6                 29

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        0      4      0      0
  11P GAIN WILD-TYPE     14     13     12     10
D21V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        0      1      3
  11P GAIN WILD-TYPE     19     18     12
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                1                 18
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P GAIN MUTATED        0      3     15      3      1      0
  11P GAIN WILD-TYPE    300     21    137     19     14      1
D21V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       10      5      3
  11P GAIN WILD-TYPE    142     83    157
D21V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               10                142
  CLUS_2                5                 83
  CLUS_3                3                157
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P GAIN MUTATED        3      1      0      0      1      4
  11P GAIN WILD-TYPE     38     36     39     12     40     20
D21V5, multiclass
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     6   3
  11P GAIN WILD-TYPE 115  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      6    3
  11P GAIN WILD-TYPE  115   70
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                115
  CLUS_2                3                 70
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED       17      0      2      3
  11P GAIN WILD-TYPE    157     86    113    127
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               17                157
  CLUS_2                0                 86
  CLUS_3                2                113
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       18      0      4
  11P GAIN WILD-TYPE    221     84    178
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               18                221
  CLUS_2                0                 84
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P GAIN MUTATED       13      3      2      2      2
  11P GAIN WILD-TYPE    136    135     47     51    114
D21V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        1      4     17
  11P GAIN WILD-TYPE     12    210    261
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                4                210
  CLUS_3               17                261
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED       11      2      3
  11P GAIN WILD-TYPE    165     88    113
D21V11, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1               11                165
  CLUS_2                2                 88
  CLUS_3                3                113
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        5      7      3      1
  11P GAIN WILD-TYPE     96     93    143     34
D21V12, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                 96
  CLUS_2                7                 93
  CLUS_3                3                143
  CLUS_4                1                 34

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        0      2      0      0
  11Q GAIN WILD-TYPE     14     15     12     10
D22V1, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        0      1      1
  11Q GAIN WILD-TYPE     19     18     14
D22V2, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q GAIN MUTATED        0      4     12      2      1      0
  11Q GAIN WILD-TYPE    300     20    140     20     14      1
D22V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       10      3      3
  11Q GAIN WILD-TYPE    142     85    157
D22V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               10                142
  CLUS_2                3                 85
  CLUS_3                3                157
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q GAIN MUTATED        3      1      0      0      1      3
  11Q GAIN WILD-TYPE     38     36     39     12     40     21
D22V5, multiclass
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     6   2
  11Q GAIN WILD-TYPE 115  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    2
  11Q GAIN WILD-TYPE  115   71
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                115
  CLUS_2                2                 71
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED       14      0      2      3
  11Q GAIN WILD-TYPE    160     86    113    127
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               14                160
  CLUS_2                0                 86
  CLUS_3                2                113
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED       15      0      4
  11Q GAIN WILD-TYPE    224     84    178
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1               15                224
  CLUS_2                0                 84
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED       10      4      2      2      1
  11Q GAIN WILD-TYPE    139    134     47     51    115
D22V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        1      5     13
  11Q GAIN WILD-TYPE     12    209    265
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                5                209
  CLUS_3               13                265
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        8      3      3
  11Q GAIN WILD-TYPE    168     87    113
D22V11, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                168
  CLUS_2                3                 87
  CLUS_3                3                113
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        4      6      3      1
  11Q GAIN WILD-TYPE     97     94    143     34
D22V12, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 97
  CLUS_2                6                 94
  CLUS_3                3                143
  CLUS_4                1                 34

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED        1      2      3      0
  12P GAIN WILD-TYPE     13     15      9     10
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 15
  CLUS_3                3                  9
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        2      2      2
  12P GAIN WILD-TYPE     17     17     13
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                2                 17
  CLUS_3                2                 13
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P GAIN MUTATED       12      8     35      9      1      0
  12P GAIN WILD-TYPE    288     16    117     13     14      1
D23V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       31     13      7
  12P GAIN WILD-TYPE    121     75    153
D23V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               31                121
  CLUS_2               13                 75
  CLUS_3                7                153
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P GAIN MUTATED        4      5      4      0      4      3
  12P GAIN WILD-TYPE     37     32     35     12     37     21
D23V5, multiclass
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    12   8
  12P GAIN WILD-TYPE 109  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     12    8
  12P GAIN WILD-TYPE  109   65
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                109
  CLUS_2                8                 65
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED       39     10      7      8
  12P GAIN WILD-TYPE    135     76    108    122
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               39                135
  CLUS_2               10                 76
  CLUS_3                7                108
  CLUS_4                8                122
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       47      5     12
  12P GAIN WILD-TYPE    192     79    170
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               47                192
  CLUS_2                5                 79
  CLUS_3               12                170
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P GAIN MUTATED       28      8     11      7     11
  12P GAIN WILD-TYPE    121    130     38     46    105
D23V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED        0     17     48
  12P GAIN WILD-TYPE     13    197    230
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2               17                197
  CLUS_3               48                230
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P GAIN MUTATED       32     11      5
  12P GAIN WILD-TYPE    144     79    111
D23V11, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               32                144
  CLUS_2               11                 79
  CLUS_3                5                111
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P GAIN MUTATED       15     22      7      4
  12P GAIN WILD-TYPE     86     78    139     31
D23V12, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               15                 86
  CLUS_2               22                 78
  CLUS_3                7                139
  CLUS_4                4                 31

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED        1      2      3      0
  12Q GAIN WILD-TYPE     13     15      9     10
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 15
  CLUS_3                3                  9
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        2      2      2
  12Q GAIN WILD-TYPE     17     17     13
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                2                 17
  CLUS_3                2                 13
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q GAIN MUTATED       12      7     21      9      1      0
  12Q GAIN WILD-TYPE    288     17    131     13     14      1
D24V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       20     11      7
  12Q GAIN WILD-TYPE    132     77    153
D24V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               20                132
  CLUS_2               11                 77
  CLUS_3                7                153
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q GAIN MUTATED        4      4      4      0      3      2
  12Q GAIN WILD-TYPE     37     33     35     12     38     22
D24V5, multiclass
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10   7
  12Q GAIN WILD-TYPE 111  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10    7
  12Q GAIN WILD-TYPE  111   66
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               10                111
  CLUS_2                7                 66
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED       26      9      6      8
  12Q GAIN WILD-TYPE    148     77    109    122
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               26                148
  CLUS_2                9                 77
  CLUS_3                6                109
  CLUS_4                8                122
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       33      4     12
  12Q GAIN WILD-TYPE    206     80    170
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               33                206
  CLUS_2                4                 80
  CLUS_3               12                170
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q GAIN MUTATED       18      8      8      5     11
  12Q GAIN WILD-TYPE    131    130     41     48    105
D24V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED        0     16     34
  12Q GAIN WILD-TYPE     13    198    244
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2               16                198
  CLUS_3               34                244
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q GAIN MUTATED       22      8      5
  12Q GAIN WILD-TYPE    154     82    111
D24V11, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               22                154
  CLUS_2                8                 82
  CLUS_3                5                111
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q GAIN MUTATED       11     15      7      2
  12Q GAIN WILD-TYPE     90     85    139     33
D24V12, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               11                 90
  CLUS_2               15                 85
  CLUS_3                7                139
  CLUS_4                2                 33

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        0      3      0      0
  13Q GAIN WILD-TYPE     14     14     12     10
D25V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        0      0      3
  13Q GAIN WILD-TYPE     19     19     12
D25V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q GAIN MUTATED        1      1     25      0      1      0
  13Q GAIN WILD-TYPE    299     23    127     22     14      1
D25V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       16      7      1
  13Q GAIN WILD-TYPE    136     81    159
D25V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               16                136
  CLUS_2                7                 81
  CLUS_3                1                159
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q GAIN MUTATED        2      2      0      0      1      3
  13Q GAIN WILD-TYPE     39     35     39     12     40     21
D25V5, multiclass
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   4
  13Q GAIN WILD-TYPE 117  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    4
  13Q GAIN WILD-TYPE  117   69
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                117
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED       24      2      0      2
  13Q GAIN WILD-TYPE    150     84    115    128
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               24                150
  CLUS_2                2                 84
  CLUS_3                0                115
  CLUS_4                2                128
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       26      0      2
  13Q GAIN WILD-TYPE    213     84    180
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               26                213
  CLUS_2                0                 84
  CLUS_3                2                180
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q GAIN MUTATED       21      2      2      0      3
  13Q GAIN WILD-TYPE    128    136     47     53    113
D25V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        0      2     26
  13Q GAIN WILD-TYPE     13    212    252
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                212
  CLUS_3               26                252
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED       15      6      2
  13Q GAIN WILD-TYPE    161     84    114
D25V11, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               15                161
  CLUS_2                6                 84
  CLUS_3                2                114
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        9     11      2      1
  13Q GAIN WILD-TYPE     92     89    144     34
D25V12, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                9                 92
  CLUS_2               11                 89
  CLUS_3                2                144
  CLUS_4                1                 34

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        1      1      1      0
  14Q GAIN WILD-TYPE     13     16     11     10
D26V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 16
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1      2      0
  14Q GAIN WILD-TYPE     18     17     15
D26V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                2                 17
  CLUS_3                0                 15
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q GAIN MUTATED        4      2     24      3      3      0
  14Q GAIN WILD-TYPE    296     22    128     19     12      1
D26V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       21      5      7
  14Q GAIN WILD-TYPE    131     83    153
D26V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               21                131
  CLUS_2                5                 83
  CLUS_3                7                153
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q GAIN MUTATED        2      0      0      1      0      1
  14Q GAIN WILD-TYPE     39     37     39     11     41     23
D26V5, multiclass
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3   1
  14Q GAIN WILD-TYPE 118  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    1
  14Q GAIN WILD-TYPE  118   72
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                1                 72
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED       27      0      2      6
  14Q GAIN WILD-TYPE    147     86    113    124
D26V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               27                147
  CLUS_2                0                 86
  CLUS_3                2                113
  CLUS_4                6                124
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       29      0      6
  14Q GAIN WILD-TYPE    210     84    176
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               29                210
  CLUS_2                0                 84
  CLUS_3                6                176
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  14Q GAIN MUTATED       21      7      5      2      1
  14Q GAIN WILD-TYPE    128    131     44     51    115
D26V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED        1      8     27
  14Q GAIN WILD-TYPE     12    206    251
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                8                206
  CLUS_3               27                251
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q GAIN MUTATED       19      7      7
  14Q GAIN WILD-TYPE    157     83    109
D26V11, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1               19                157
  CLUS_2                7                 83
  CLUS_3                7                109
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q GAIN MUTATED        9     15      7      2
  14Q GAIN WILD-TYPE     92     85    139     33
D26V12, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                9                 92
  CLUS_2               15                 85
  CLUS_3                7                139
  CLUS_4                2                 33

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        0      0      0      0
  15Q GAIN WILD-TYPE     14     17     12     10
D27V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        0      0      0
  15Q GAIN WILD-TYPE     19     19     15
D27V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q GAIN MUTATED        1      0      6      3      0      0
  15Q GAIN WILD-TYPE    299     24    146     19     15      1
D27V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        3      2      4
  15Q GAIN WILD-TYPE    149     86    156
D27V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                149
  CLUS_2                2                 86
  CLUS_3                4                156
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q GAIN MUTATED        1      0      0      0      0      1
  15Q GAIN WILD-TYPE     40     37     39     12     41     23
D27V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11N         TCGA-B5-A11Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1   1
  15Q GAIN WILD-TYPE 120  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    1
  15Q GAIN WILD-TYPE  120   72
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                1                 72
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        4      1      2      3
  15Q GAIN WILD-TYPE    170     85    113    127
D27V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                170
  CLUS_2                1                 85
  CLUS_3                2                113
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        6      0      4
  15Q GAIN WILD-TYPE    233     84    178
D27V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                233
  CLUS_2                0                 84
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q GAIN MUTATED        3      2      2      2      1
  15Q GAIN WILD-TYPE    146    136     47     51    115
D27V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        0      3      7
  15Q GAIN WILD-TYPE     13    211    271
D27V10, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                211
  CLUS_3                7                271
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q GAIN MUTATED        3      1      4
  15Q GAIN WILD-TYPE    173     89    112
D27V11, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                173
  CLUS_2                1                 89
  CLUS_3                4                112
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q GAIN MUTATED        2      1      4      1
  15Q GAIN WILD-TYPE     99     99    142     34
D27V12, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 99
  CLUS_2                1                 99
  CLUS_3                4                142
  CLUS_4                1                 34

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        0      1      0      0
  16P GAIN WILD-TYPE     14     16     12     10
D28V1, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        0      0      1
  16P GAIN WILD-TYPE     19     19     14
D28V2, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P GAIN MUTATED        1      1     17      3      1      0
  16P GAIN WILD-TYPE    299     23    135     19     14      1
D28V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       13      0      8
  16P GAIN WILD-TYPE    139     88    152
D28V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               13                139
  CLUS_2                0                 88
  CLUS_3                8                152
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P GAIN MUTATED        1      1      0      0      3      3
  16P GAIN WILD-TYPE     40     36     39     12     38     21
D28V5, multiclass
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     6   2
  16P GAIN WILD-TYPE 115  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    2
  16P GAIN WILD-TYPE  115   71
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                115
  CLUS_2                2                 71
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED       14      2      3      4
  16P GAIN WILD-TYPE    160     84    112    126
D28V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               14                160
  CLUS_2                2                 84
  CLUS_3                3                112
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED       15      1      7
  16P GAIN WILD-TYPE    224     83    175
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               15                224
  CLUS_2                1                 83
  CLUS_3                7                175
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P GAIN MUTATED       13      3      2      2      3
  16P GAIN WILD-TYPE    136    135     47     51    113
D28V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        1      7     15
  16P GAIN WILD-TYPE     12    207    263
D28V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                7                207
  CLUS_3               15                263
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P GAIN MUTATED        9      4      5
  16P GAIN WILD-TYPE    167     86    111
D28V11, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                9                167
  CLUS_2                4                 86
  CLUS_3                5                111
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P GAIN MUTATED        6      6      6      0
  16P GAIN WILD-TYPE     95     94    140     35
D28V12, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                 95
  CLUS_2                6                 94
  CLUS_3                6                140
  CLUS_4                0                 35

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        0      0      0      0
  16Q GAIN WILD-TYPE     14     17     12     10
D29V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        0      0      0
  16Q GAIN WILD-TYPE     19     19     15
D29V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q GAIN MUTATED        0      1      7      2      0      0
  16Q GAIN WILD-TYPE    300     23    145     20     15      1
D29V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        5      1      3
  16Q GAIN WILD-TYPE    147     87    157
D29V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                147
  CLUS_2                1                 87
  CLUS_3                3                157
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q GAIN MUTATED        1      1      0      0      1      0
  16Q GAIN WILD-TYPE     40     36     39     12     40     24
D29V5, multiclass
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1   2
  16Q GAIN WILD-TYPE 120  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    2
  16Q GAIN WILD-TYPE  120   71
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                2                 71
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        6      0      1      2
  16Q GAIN WILD-TYPE    168     86    114    128
D29V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                168
  CLUS_2                0                 86
  CLUS_3                1                114
  CLUS_4                2                128
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        6      0      3
  16Q GAIN WILD-TYPE    233     84    179
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                233
  CLUS_2                0                 84
  CLUS_3                3                179
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q GAIN MUTATED        5      2      0      0      3
  16Q GAIN WILD-TYPE    144    136     49     53    113
D29V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        0      3      7
  16Q GAIN WILD-TYPE     13    211    271
D29V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                211
  CLUS_3                7                271
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q GAIN MUTATED        3      2      2
  16Q GAIN WILD-TYPE    173     88    114
D29V11, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                173
  CLUS_2                2                 88
  CLUS_3                2                114
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q GAIN MUTATED        3      2      2      0
  16Q GAIN WILD-TYPE     98     98    144     35
D29V12, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 98
  CLUS_2                2                 98
  CLUS_3                2                144
  CLUS_4                0                 35

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        0      1      0      0
  17P GAIN WILD-TYPE     14     16     12     10
D30V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        0      0      1
  17P GAIN WILD-TYPE     19     19     14
D30V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P GAIN MUTATED        1      1      8      1      1      0
  17P GAIN WILD-TYPE    299     23    144     21     14      1
D30V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        6      2      2
  17P GAIN WILD-TYPE    146     86    158
D30V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                146
  CLUS_2                2                 86
  CLUS_3                2                158
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P GAIN MUTATED        1      1      0      1      0      0
  17P GAIN WILD-TYPE     40     36     39     11     41     24
D30V5, multiclass
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1   2
  17P GAIN WILD-TYPE 120  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    2
  17P GAIN WILD-TYPE  120   71
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                2                 71
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        9      2      1      0
  17P GAIN WILD-TYPE    165     84    114    130
D30V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                9                165
  CLUS_2                2                 84
  CLUS_3                1                114
  CLUS_4                0                130
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED       11      1      0
  17P GAIN WILD-TYPE    228     83    182
D30V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               11                228
  CLUS_2                1                 83
  CLUS_3                0                182
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P GAIN MUTATED        7      1      1      1      2
  17P GAIN WILD-TYPE    142    137     48     52    114
D30V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        0      2     10
  17P GAIN WILD-TYPE     13    212    268
D30V10, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                212
  CLUS_3               10                268
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P GAIN MUTATED        6      2      2
  17P GAIN WILD-TYPE    170     88    114
D30V11, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                6                170
  CLUS_2                2                 88
  CLUS_3                2                114
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P GAIN MUTATED        5      3      2      0
  17P GAIN WILD-TYPE     96     97    144     35
D30V12, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                 96
  CLUS_2                3                 97
  CLUS_3                2                144
  CLUS_4                0                 35

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        0      1      0      0
  17Q GAIN WILD-TYPE     14     16     12     10
D31V1, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        0      0      1
  17Q GAIN WILD-TYPE     19     19     14
D31V2, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q GAIN MUTATED        1      3     22      1      1      0
  17Q GAIN WILD-TYPE    299     21    130     21     14      1
D31V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       20      3      2
  17Q GAIN WILD-TYPE    132     85    158
D31V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               20                132
  CLUS_2                3                 85
  CLUS_3                2                158
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q GAIN MUTATED        4      1      0      1      0      0
  17Q GAIN WILD-TYPE     37     36     39     11     41     24
D31V5, multiclass
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3   3
  17Q GAIN WILD-TYPE 118  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    3
  17Q GAIN WILD-TYPE  118   70
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                3                 70
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED       21      4      1      2
  17Q GAIN WILD-TYPE    153     82    114    128
D31V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               21                153
  CLUS_2                4                 82
  CLUS_3                1                114
  CLUS_4                2                128
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       25      1      2
  17Q GAIN WILD-TYPE    214     83    180
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               25                214
  CLUS_2                1                 83
  CLUS_3                2                180
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q GAIN MUTATED       18      3      4      1      2
  17Q GAIN WILD-TYPE    131    135     45     52    114
D31V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        0      5     23
  17Q GAIN WILD-TYPE     13    209    255
D31V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                209
  CLUS_3               23                255
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED       16      5      3
  17Q GAIN WILD-TYPE    160     85    113
D31V11, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               16                160
  CLUS_2                5                 85
  CLUS_3                3                113
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        9     11      3      1
  17Q GAIN WILD-TYPE     92     89    143     34
D31V12, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                 92
  CLUS_2               11                 89
  CLUS_3                3                143
  CLUS_4                1                 34

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED        1      4      1      0
  18P GAIN WILD-TYPE     13     13     11     10
D32V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                4                 13
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        1      1      4
  18P GAIN WILD-TYPE     18     18     11
D32V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                1                 18
  CLUS_3                4                 11
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P GAIN MUTATED        3      4     56      1      1      0
  18P GAIN WILD-TYPE    297     20     96     21     14      1
D32V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       39     13      3
  18P GAIN WILD-TYPE    113     75    157
D32V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               39                113
  CLUS_2               13                 75
  CLUS_3                3                157
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P GAIN MUTATED        7      3      0      0      1      4
  18P GAIN WILD-TYPE     34     34     39     12     40     20
D32V5, multiclass
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5  10
  18P GAIN WILD-TYPE 116  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   10
  18P GAIN WILD-TYPE  116   63
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                116
  CLUS_2               10                 63
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED       52      6      2      4
  18P GAIN WILD-TYPE    122     80    113    126
D32V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               52                122
  CLUS_2                6                 80
  CLUS_3                2                113
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       58      1      5
  18P GAIN WILD-TYPE    181     83    177
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               58                181
  CLUS_2                1                 83
  CLUS_3                5                177
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P GAIN MUTATED       43      2      9      6      5
  18P GAIN WILD-TYPE    106    136     40     47    111
D32V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED        0      5     60
  18P GAIN WILD-TYPE     13    209    218
D32V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                209
  CLUS_3               60                218
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P GAIN MUTATED       37     14      2
  18P GAIN WILD-TYPE    139     76    114
D32V11, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               37                139
  CLUS_2               14                 76
  CLUS_3                2                114
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P GAIN MUTATED       20     30      2      1
  18P GAIN WILD-TYPE     81     70    144     34
D32V12, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1               20                 81
  CLUS_2               30                 70
  CLUS_3                2                144
  CLUS_4                1                 34

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED        0      3      1      0
  18Q GAIN WILD-TYPE     14     14     11     10
D33V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        0      1      3
  18Q GAIN WILD-TYPE     19     18     12
D33V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                1                 18
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q GAIN MUTATED        3      3     33      0      1      0
  18Q GAIN WILD-TYPE    297     21    119     22     14      1
D33V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       22     10      2
  18Q GAIN WILD-TYPE    130     78    158
D33V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               22                130
  CLUS_2               10                 78
  CLUS_3                2                158
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q GAIN MUTATED        4      2      0      0      1      2
  18Q GAIN WILD-TYPE     37     35     39     12     40     22
D33V5, multiclass
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3   6
  18Q GAIN WILD-TYPE 118  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    6
  18Q GAIN WILD-TYPE  118   67
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                6                 67
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED       32      2      2      3
  18Q GAIN WILD-TYPE    142     84    113    127
D33V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               32                142
  CLUS_2                2                 84
  CLUS_3                2                113
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       35      0      4
  18Q GAIN WILD-TYPE    204     84    178
D33V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               35                204
  CLUS_2                0                 84
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q GAIN MUTATED       27      1      5      6      1
  18Q GAIN WILD-TYPE    122    137     44     47    115
D33V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED        0      3     37
  18Q GAIN WILD-TYPE     13    211    241
D33V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                211
  CLUS_3               37                241
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q GAIN MUTATED       24      7      1
  18Q GAIN WILD-TYPE    152     83    115
D33V11, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               24                152
  CLUS_2                7                 83
  CLUS_3                1                115
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q GAIN MUTATED       10     20      1      1
  18Q GAIN WILD-TYPE     91     80    145     34
D33V12, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1               10                 91
  CLUS_2               20                 80
  CLUS_3                1                145
  CLUS_4                1                 34

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        0      4      0      0
  19P GAIN WILD-TYPE     14     13     12     10
D34V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        0      0      4
  19P GAIN WILD-TYPE     19     19     11
D34V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                4                 11
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P GAIN MUTATED        0      1     47      0      2      0
  19P GAIN WILD-TYPE    300     23    105     22     13      1
D34V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       27     11      7
  19P GAIN WILD-TYPE    125     77    153
D34V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               27                125
  CLUS_2               11                 77
  CLUS_3                7                153
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P GAIN MUTATED        3      2      1      0      1      1
  19P GAIN WILD-TYPE     38     35     38     12     40     23
D34V5, multiclass
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3   5
  19P GAIN WILD-TYPE 118  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    5
  19P GAIN WILD-TYPE  118   68
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                118
  CLUS_2                5                 68
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED       41      2      2      4
  19P GAIN WILD-TYPE    133     84    113    126
D34V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               41                133
  CLUS_2                2                 84
  CLUS_3                2                113
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       44      1      4
  19P GAIN WILD-TYPE    195     83    178
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               44                195
  CLUS_2                1                 83
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P GAIN MUTATED       33      5      7      2      3
  19P GAIN WILD-TYPE    116    133     42     51    113
D34V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        2      8     40
  19P GAIN WILD-TYPE     11    206    238
D34V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                8                206
  CLUS_3               40                238
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED       24     13      6
  19P GAIN WILD-TYPE    152     77    110
D34V11, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               24                152
  CLUS_2               13                 77
  CLUS_3                6                110
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED       15     16     10      2
  19P GAIN WILD-TYPE     86     84    136     33
D34V12, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1               15                 86
  CLUS_2               16                 84
  CLUS_3               10                136
  CLUS_4                2                 33

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        0      2      0      0
  19Q GAIN WILD-TYPE     14     15     12     10
D35V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        0      0      2
  19Q GAIN WILD-TYPE     19     19     13
D35V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q GAIN MUTATED        0      2     50      1      2      0
  19Q GAIN WILD-TYPE    300     22    102     21     13      1
D35V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       30     13      6
  19Q GAIN WILD-TYPE    122     75    154
D35V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               30                122
  CLUS_2               13                 75
  CLUS_3                6                154
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q GAIN MUTATED        1      2      1      0      1      3
  19Q GAIN WILD-TYPE     40     35     38     12     40     21
D35V5, multiclass
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4   4
  19Q GAIN WILD-TYPE 117  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4    4
  19Q GAIN WILD-TYPE  117   69
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                117
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED       46      4      2      3
  19Q GAIN WILD-TYPE    128     82    113    127
D35V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               46                128
  CLUS_2                4                 82
  CLUS_3                2                113
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       52      0      3
  19Q GAIN WILD-TYPE    187     84    179
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               52                187
  CLUS_2                0                 84
  CLUS_3                3                179
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED       38      4      7      3      3
  19Q GAIN WILD-TYPE    111    134     42     50    113
D35V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        1      6     48
  19Q GAIN WILD-TYPE     12    208    230
D35V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                6                208
  CLUS_3               48                230
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED       27     15      5
  19Q GAIN WILD-TYPE    149     75    111
D35V11, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               27                149
  CLUS_2               15                 75
  CLUS_3                5                111
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED       15     22      8      2
  19Q GAIN WILD-TYPE     86     78    138     33
D35V12, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               15                 86
  CLUS_2               22                 78
  CLUS_3                8                138
  CLUS_4                2                 33

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED        0      5      0      0
  20P GAIN WILD-TYPE     14     12     12     10
D36V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                5                 12
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        0      0      5
  20P GAIN WILD-TYPE     19     19     10
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                5                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P GAIN MUTATED        6      7     76     16      1      0
  20P GAIN WILD-TYPE    294     17     76      6     14      1
D36V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       65     15     17
  20P GAIN WILD-TYPE     87     73    143
D36V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               65                 87
  CLUS_2               15                 73
  CLUS_3               17                143
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P GAIN MUTATED        5      6      2      0      2      5
  20P GAIN WILD-TYPE     36     31     37     12     39     19
D36V5, multiclass
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    12   8
  20P GAIN WILD-TYPE 109  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12    8
  20P GAIN WILD-TYPE  109   65
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               12                109
  CLUS_2                8                 65
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED       73     11      8     14
  20P GAIN WILD-TYPE    101     75    107    116
D36V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               73                101
  CLUS_2               11                 75
  CLUS_3                8                107
  CLUS_4               14                116
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       84      3     19
  20P GAIN WILD-TYPE    155     81    163
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               84                155
  CLUS_2                3                 81
  CLUS_3               19                163
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P GAIN MUTATED       62     15     11      8      9
  20P GAIN WILD-TYPE     87    123     38     45    107
D36V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED        2     20     83
  20P GAIN WILD-TYPE     11    194    195
D36V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2               20                194
  CLUS_3               83                195
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P GAIN MUTATED       61     16     15
  20P GAIN WILD-TYPE    115     74    101
D36V11, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               61                115
  CLUS_2               16                 74
  CLUS_3               15                101
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P GAIN MUTATED       20     47     20      5
  20P GAIN WILD-TYPE     81     53    126     30
D36V12, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               20                 81
  CLUS_2               47                 53
  CLUS_3               20                126
  CLUS_4                5                 30

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED        0      6      0      0
  20Q GAIN WILD-TYPE     14     11     12     10
D37V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        0      0      6
  20Q GAIN WILD-TYPE     19     19      9
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                6                  9
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q GAIN MUTATED        7      7     90     18      1      0
  20Q GAIN WILD-TYPE    293     17     62      4     14      1
D37V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       73     18     20
  20Q GAIN WILD-TYPE     79     70    140
D37V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               73                 79
  CLUS_2               18                 70
  CLUS_3               20                140
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q GAIN MUTATED        6      8      2      0      2      6
  20Q GAIN WILD-TYPE     35     29     37     12     39     18
D37V5, multiclass
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    13  11
  20Q GAIN WILD-TYPE 108  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     13   11
  20Q GAIN WILD-TYPE  108   62
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               13                108
  CLUS_2               11                 62
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED       84     13      9     17
  20Q GAIN WILD-TYPE     90     73    106    113
D37V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               84                 90
  CLUS_2               13                 73
  CLUS_3                9                106
  CLUS_4               17                113
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       96      4     23
  20Q GAIN WILD-TYPE    143     80    159
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               96                143
  CLUS_2                4                 80
  CLUS_3               23                159
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q GAIN MUTATED       71     18     12      8     12
  20Q GAIN WILD-TYPE     78    120     37     45    104
D37V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED        2     24     95
  20Q GAIN WILD-TYPE     11    190    183
D37V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2               24                190
  CLUS_3               95                183
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q GAIN MUTATED       67     20     19
  20Q GAIN WILD-TYPE    109     70     97
D37V11, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               67                109
  CLUS_2               20                 70
  CLUS_3               19                 97
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q GAIN MUTATED       24     52     24      6
  20Q GAIN WILD-TYPE     77     48    122     29
D37V12, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               24                 77
  CLUS_2               52                 48
  CLUS_3               24                122
  CLUS_4                6                 29

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        1      1      0      0
  21Q GAIN WILD-TYPE     13     16     12     10
D38V1, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        1      0      1
  21Q GAIN WILD-TYPE     18     19     14
D38V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q GAIN MUTATED        1      0     32      2      1      0
  21Q GAIN WILD-TYPE    299     24    120     20     14      1
D38V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       20      8      5
  21Q GAIN WILD-TYPE    132     80    155
D38V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               20                132
  CLUS_2                8                 80
  CLUS_3                5                155
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q GAIN MUTATED        1      2      0      0      0      1
  21Q GAIN WILD-TYPE     40     35     39     12     41     23
D38V5, multiclass
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1   3
  21Q GAIN WILD-TYPE 120  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    3
  21Q GAIN WILD-TYPE  120   70
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                120
  CLUS_2                3                 70
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED       28      3      1      4
  21Q GAIN WILD-TYPE    146     83    114    126
D38V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               28                146
  CLUS_2                3                 83
  CLUS_3                1                114
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       31      1      4
  21Q GAIN WILD-TYPE    208     83    178
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               31                208
  CLUS_2                1                 83
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED       25      3      5      1      2
  21Q GAIN WILD-TYPE    124    135     44     52    114
D38V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        0      4     32
  21Q GAIN WILD-TYPE     13    210    246
D38V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                210
  CLUS_3               32                246
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED       19      8      5
  21Q GAIN WILD-TYPE    157     82    111
D38V11, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               19                157
  CLUS_2                8                 82
  CLUS_3                5                111
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED       12     14      6      0
  21Q GAIN WILD-TYPE     89     86    140     35
D38V12, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               12                 89
  CLUS_2               14                 86
  CLUS_3                6                140
  CLUS_4                0                 35

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        1      1      0      0
  22Q GAIN WILD-TYPE     13     16     12     10
D39V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05D         TCGA-AP-A05H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        1      0      1
  22Q GAIN WILD-TYPE     18     19     14
D39V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05D         TCGA-AP-A05H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q GAIN MUTATED        3      4     24      0      0      0
  22Q GAIN WILD-TYPE    297     20    128     22     15      1
D39V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED       26      1      1
  22Q GAIN WILD-TYPE    126     87    159
D39V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               26                126
  CLUS_2                1                 87
  CLUS_3                1                159
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q GAIN MUTATED        1      2      0      0      0      0
  22Q GAIN WILD-TYPE     40     35     39     12     41     24
D39V5, multiclass
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   3
  22Q GAIN WILD-TYPE 121  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    3
  22Q GAIN WILD-TYPE  121   70
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                121
  CLUS_2                3                 70
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED       27      4      0      0
  22Q GAIN WILD-TYPE    147     82    115    130
D39V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               27                147
  CLUS_2                4                 82
  CLUS_3                0                115
  CLUS_4                0                130
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED       31      0      0
  22Q GAIN WILD-TYPE    208     84    182
D39V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               31                208
  CLUS_2                0                 84
  CLUS_3                0                182
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q GAIN MUTATED       19      1      3      0      7
  22Q GAIN WILD-TYPE    130    137     46     53    109
D39V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        0      2     28
  22Q GAIN WILD-TYPE     13    212    250
D39V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                212
  CLUS_3               28                250
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED       25      2      1
  22Q GAIN WILD-TYPE    151     88    115
D39V11, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1               25                151
  CLUS_2                2                 88
  CLUS_3                1                115
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        6     20      1      1
  22Q GAIN WILD-TYPE     95     80    145     34
D39V12, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                 95
  CLUS_2               20                 80
  CLUS_3                1                145
  CLUS_4                1                 34

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        1      2      2      0
  XQ GAIN WILD-TYPE     13     15     10     10
D40V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                15
  CLUS_3               2                10
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        2      1      2
  XQ GAIN WILD-TYPE     17     18     13
D40V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               1                18
  CLUS_3               2                13
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ GAIN MUTATED        8     12     22      7     12      0
  XQ GAIN WILD-TYPE    292     12    130     15      3      1
D40V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       19     10     16
  XQ GAIN WILD-TYPE    133     78    144
D40V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              19               133
  CLUS_2              10                78
  CLUS_3              16               144
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ GAIN MUTATED        3      4      4      2      3      3
  XQ GAIN WILD-TYPE     38     33     35     10     38     21
D40V5, multiclass
D40V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14   5
  XQ GAIN WILD-TYPE 107  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14    5
  XQ GAIN WILD-TYPE  107   68
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              14               107
  CLUS_2               5                68
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED       24      6     11     17
  XQ GAIN WILD-TYPE    150     80    104    113
D40V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              24               150
  CLUS_2               6                80
  CLUS_3              11               104
  CLUS_4              17               113
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       29      8     21
  XQ GAIN WILD-TYPE    210     76    161
D40V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              29               210
  CLUS_2               8                76
  CLUS_3              21               161
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED       22     16      5      6     12
  XQ GAIN WILD-TYPE    127    122     44     47    104
D40V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        1     26     34
  XQ GAIN WILD-TYPE     12    188    244
D40V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2              26               188
  CLUS_3              34               244
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED       26      6     14
  XQ GAIN WILD-TYPE    150     84    102
D40V11, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1              26               150
  CLUS_2               6                84
  CLUS_3              14               102
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        9     15     18      4
  XQ GAIN WILD-TYPE     92     85    128     31
D40V12, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               9                92
  CLUS_2              15                85
  CLUS_3              18               128
  CLUS_4               4                31

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        1      1      0      0
  1P LOSS WILD-TYPE     13     16     12     10
D41V1, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      0      1
  1P LOSS WILD-TYPE     18     19     14
D41V2, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P LOSS MUTATED        0      5     17      2      0      0
  1P LOSS WILD-TYPE    300     19    135     20     15      1
D41V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       18      1      1
  1P LOSS WILD-TYPE    134     87    159
D41V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              18               134
  CLUS_2               1                87
  CLUS_3               1               159
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1P LOSS MUTATED        2      1      0      0      1      0
  1P LOSS WILD-TYPE     39     36     39     12     40     24
D41V5, multiclass
D41V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   3
  1P LOSS WILD-TYPE 120  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    3
  1P LOSS WILD-TYPE  120   70
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               3                70
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED       20      2      1      1
  1P LOSS WILD-TYPE    154     84    114    129
D41V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              20               154
  CLUS_2               2                84
  CLUS_3               1               114
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       22      0      2
  1P LOSS WILD-TYPE    217     84    180
D41V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              22               217
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P LOSS MUTATED       13      2      2      3      4
  1P LOSS WILD-TYPE    136    136     47     50    112
D41V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED        1      1     22
  1P LOSS WILD-TYPE     12    213    256
D41V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1               213
  CLUS_3              22               256
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P LOSS MUTATED       13      6      2
  1P LOSS WILD-TYPE    163     84    114
D41V11, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              13               163
  CLUS_2               6                84
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P LOSS MUTATED        6     12      2      1
  1P LOSS WILD-TYPE     95     88    144     34
D41V12, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6                95
  CLUS_2              12                88
  CLUS_3               2               144
  CLUS_4               1                34

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        1      1      0      0
  1Q LOSS WILD-TYPE     13     16     12     10
D42V1, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        1      0      1
  1Q LOSS WILD-TYPE     18     19     14
D42V2, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q LOSS MUTATED        0      2     12      1      0      0
  1Q LOSS WILD-TYPE    300     22    140     21     15      1
D42V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED       11      1      1
  1Q LOSS WILD-TYPE    141     87    159
D42V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              11               141
  CLUS_2               1                87
  CLUS_3               1               159
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  1Q LOSS MUTATED        1      1      0      0      0      0
  1Q LOSS WILD-TYPE     40     36     39     12     41     24
D42V5, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G5        TCGA-A5-A0G9        TCGA-A5-A0GA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM        TCGA-AP-A0LN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D        TCGA-AX-A06F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS        TCGA-AX-A0IW 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1        TCGA-B5-A0JN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D42V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   2
  1Q LOSS WILD-TYPE 121  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    2
  1Q LOSS WILD-TYPE  121   71
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED       13      1      0      1
  1Q LOSS WILD-TYPE    161     85    115    129
D42V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              13               161
  CLUS_2               1                85
  CLUS_3               0               115
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED       14      0      1
  1Q LOSS WILD-TYPE    225     84    181
D42V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1              14               225
  CLUS_2               0                84
  CLUS_3               1               181
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1Q LOSS MUTATED        9      2      1      0      3
  1Q LOSS WILD-TYPE    140    136     48     53    113
D42V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        1      1     13
  1Q LOSS WILD-TYPE     12    213    265
D42V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               1               213
  CLUS_3              13               265
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1Q LOSS MUTATED        7      4      2
  1Q LOSS WILD-TYPE    169     86    114
D42V11, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               7               169
  CLUS_2               4                86
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1Q LOSS MUTATED        3      7      2      1
  1Q LOSS WILD-TYPE     98     93    144     34
D42V12, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                98
  CLUS_2               7                93
  CLUS_3               2               144
  CLUS_4               1                34

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        0      0      0      0
  2P LOSS WILD-TYPE     14     17     12     10
D43V1, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        0      0      0
  2P LOSS WILD-TYPE     19     19     15
D43V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2P LOSS MUTATED        0      0      8      2      0      0
  2P LOSS WILD-TYPE    300     24    144     20     15      1
D43V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        5      3      2
  2P LOSS WILD-TYPE    147     85    158
D43V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5               147
  CLUS_2               3                85
  CLUS_3               2               158
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2P LOSS MUTATED        1      1      0      0      0      0
  2P LOSS WILD-TYPE     40     36     39     12     41     24
D43V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   2
  2P LOSS WILD-TYPE 121  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    2
  2P LOSS WILD-TYPE  121   71
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        9      0      0      1
  2P LOSS WILD-TYPE    165     86    115    129
D43V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9               165
  CLUS_2               0                86
  CLUS_3               0               115
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        9      0      1
  2P LOSS WILD-TYPE    230     84    181
D43V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9               230
  CLUS_2               0                84
  CLUS_3               1               181
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2P LOSS MUTATED        6      2      0      2      0
  2P LOSS WILD-TYPE    143    136     49     51    116
D43V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        0      2      8
  2P LOSS WILD-TYPE     13    212    270
D43V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2               212
  CLUS_3               8               270
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2P LOSS MUTATED        5      2      2
  2P LOSS WILD-TYPE    171     88    114
D43V11, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5               171
  CLUS_2               2                88
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2P LOSS MUTATED        3      2      2      2
  2P LOSS WILD-TYPE     98     98    144     33
D43V12, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                98
  CLUS_2               2                98
  CLUS_3               2               144
  CLUS_4               2                33

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED        0      1      0      0
  2Q LOSS WILD-TYPE     14     16     12     10
D44V1, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        0      0      1
  2Q LOSS WILD-TYPE     19     19     14
D44V2, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q LOSS MUTATED        0      0     14      2      0      0
  2Q LOSS WILD-TYPE    300     24    138     20     15      1
D44V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        7      5      3
  2Q LOSS WILD-TYPE    145     83    157
D44V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               7               145
  CLUS_2               5                83
  CLUS_3               3               157
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  2Q LOSS MUTATED        1      1      0      0      0      0
  2Q LOSS WILD-TYPE     40     36     39     12     41     24
D44V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   2
  2Q LOSS WILD-TYPE 121  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    2
  2Q LOSS WILD-TYPE  121   71
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0               121
  CLUS_2               2                71
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED       14      0      0      2
  2Q LOSS WILD-TYPE    160     86    115    128
D44V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              14               160
  CLUS_2               0                86
  CLUS_3               0               115
  CLUS_4               2               128
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED       14      0      2
  2Q LOSS WILD-TYPE    225     84    180
D44V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1              14               225
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  2Q LOSS MUTATED       10      2      1      2      1
  2Q LOSS WILD-TYPE    139    136     48     51    115
D44V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        0      2     14
  2Q LOSS WILD-TYPE     13    212    264
D44V10, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2               212
  CLUS_3              14               264
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  2Q LOSS MUTATED        7      4      3
  2Q LOSS WILD-TYPE    169     86    113
D44V11, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               7               169
  CLUS_2               4                86
  CLUS_3               3               113
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  2Q LOSS MUTATED        6      3      3      2
  2Q LOSS WILD-TYPE     95     97    143     33
D44V12, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               6                95
  CLUS_2               3                97
  CLUS_3               3               143
  CLUS_4               2                33

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      4      0      0
  3P LOSS WILD-TYPE     14     13     12     10
D45V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        0      0      4
  3P LOSS WILD-TYPE     19     19     11
D45V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               0                19
  CLUS_3               4                11
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P LOSS MUTATED        0      3     43      3      0      0
  3P LOSS WILD-TYPE    300     21    109     19     15      1
D45V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       29      8      3
  3P LOSS WILD-TYPE    123     80    157
D45V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              29               123
  CLUS_2               8                80
  CLUS_3               3               157
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3P LOSS MUTATED        2      8      1      0      1      2
  3P LOSS WILD-TYPE     39     29     38     12     40     22
D45V5, multiclass
D45V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     5   9
  3P LOSS WILD-TYPE 116  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    9
  3P LOSS WILD-TYPE  116   64
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               5               116
  CLUS_2               9                64
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED       41      2      3      2
  3P LOSS WILD-TYPE    133     84    112    128
D45V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              41               133
  CLUS_2               2                84
  CLUS_3               3               112
  CLUS_4               2               128
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       45      1      2
  3P LOSS WILD-TYPE    194     83    180
D45V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              45               194
  CLUS_2               1                83
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P LOSS MUTATED       32      3      2      4      6
  3P LOSS WILD-TYPE    117    135     47     49    110
D45V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        2      5     40
  3P LOSS WILD-TYPE     11    209    238
D45V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               5               209
  CLUS_3              40               238
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED       26      8      4
  3P LOSS WILD-TYPE    150     82    112
D45V11, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              26               150
  CLUS_2               8                82
  CLUS_3               4               112
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED       10     21      4      3
  3P LOSS WILD-TYPE     91     79    142     32
D45V12, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1              10                91
  CLUS_2              21                79
  CLUS_3               4               142
  CLUS_4               3                32

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        0      4      0      0
  3Q LOSS WILD-TYPE     14     13     12     10
D46V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        0      0      4
  3Q LOSS WILD-TYPE     19     19     11
D46V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               0                19
  CLUS_3               4                11
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q LOSS MUTATED        0      2     25      2      0      0
  3Q LOSS WILD-TYPE    300     22    127     20     15      1
D46V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       17      4      2
  3Q LOSS WILD-TYPE    135     84    158
D46V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              17               135
  CLUS_2               4                84
  CLUS_3               2               158
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  3Q LOSS MUTATED        1      4      0      0      0      1
  3Q LOSS WILD-TYPE     40     33     39     12     41     23
D46V5, multiclass
D46V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   4
  3Q LOSS WILD-TYPE 119  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    4
  3Q LOSS WILD-TYPE  119   69
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               4                69
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED       24      1      1      2
  3Q LOSS WILD-TYPE    150     85    114    128
D46V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              24               150
  CLUS_2               1                85
  CLUS_3               1               114
  CLUS_4               2               128
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       26      0      2
  3Q LOSS WILD-TYPE    213     84    180
D46V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              26               213
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q LOSS MUTATED       18      3      2      0      4
  3Q LOSS WILD-TYPE    131    135     47     53    112
D46V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        1      4     22
  3Q LOSS WILD-TYPE     12    210    256
D46V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               4               210
  CLUS_3              22               256
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED       14      6      3
  3Q LOSS WILD-TYPE    162     84    113
D46V11, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1              14               162
  CLUS_2               6                84
  CLUS_3               3               113
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        8     11      3      1
  3Q LOSS WILD-TYPE     93     89    143     34
D46V12, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8                93
  CLUS_2              11                89
  CLUS_3               3               143
  CLUS_4               1                34

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED        1      7      0      0
  4P LOSS WILD-TYPE     13     10     12     10
D47V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               7                10
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED        1      0      7
  4P LOSS WILD-TYPE     18     19      8
D47V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               7                 8
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P LOSS MUTATED        4      9     80      4      1      0
  4P LOSS WILD-TYPE    296     15     72     18     14      1
D47V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       63     18      6
  4P LOSS WILD-TYPE     89     70    154
D47V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              63                89
  CLUS_2              18                70
  CLUS_3               6               154
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4P LOSS MUTATED        5      8      0      1      1      6
  4P LOSS WILD-TYPE     36     29     39     11     40     18
D47V5, multiclass
D47V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11  10
  4P LOSS WILD-TYPE 110  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11   10
  4P LOSS WILD-TYPE  110   63
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              11               110
  CLUS_2              10                63
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED       77      9      6      6
  4P LOSS WILD-TYPE     97     77    109    124
D47V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              77                97
  CLUS_2               9                77
  CLUS_3               6               109
  CLUS_4               6               124
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       87      2      9
  4P LOSS WILD-TYPE    152     82    173
D47V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              87               152
  CLUS_2               2                82
  CLUS_3               9               173
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P LOSS MUTATED       66      7     10      8      5
  4P LOSS WILD-TYPE     83    131     39     45    111
D47V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED        2      9     85
  4P LOSS WILD-TYPE     11    205    193
D47V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               9               205
  CLUS_3              85               193
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P LOSS MUTATED       56     22      9
  4P LOSS WILD-TYPE    120     68    107
D47V11, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              56               120
  CLUS_2              22                68
  CLUS_3               9               107
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P LOSS MUTATED       29     41     11      6
  4P LOSS WILD-TYPE     72     59    135     29
D47V12, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              29                72
  CLUS_2              41                59
  CLUS_3              11               135
  CLUS_4               6                29

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED        1      4      0      0
  4Q LOSS WILD-TYPE     13     13     12     10
D48V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED        1      0      4
  4Q LOSS WILD-TYPE     18     19     11
D48V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               4                11
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q LOSS MUTATED        3      8     81      4      1      0
  4Q LOSS WILD-TYPE    297     16     71     18     14      1
D48V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED       62     18      5
  4Q LOSS WILD-TYPE     90     70    155
D48V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              62                90
  CLUS_2              18                70
  CLUS_3               5               155
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  4Q LOSS MUTATED        5      7      1      1      1      6
  4Q LOSS WILD-TYPE     36     30     38     11     40     18
D48V5, multiclass
D48V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    11  10
  4Q LOSS WILD-TYPE 110  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11   10
  4Q LOSS WILD-TYPE  110   63
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11               110
  CLUS_2              10                63
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED       79      7      5      6
  4Q LOSS WILD-TYPE     95     79    110    124
D48V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              79                95
  CLUS_2               7                79
  CLUS_3               5               110
  CLUS_4               6               124
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED       86      2      9
  4Q LOSS WILD-TYPE    153     82    173
D48V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              86               153
  CLUS_2               2                82
  CLUS_3               9               173
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q LOSS MUTATED       60      8     12      8      7
  4Q LOSS WILD-TYPE     89    130     37     45    109
D48V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED        2      8     85
  4Q LOSS WILD-TYPE     11    206    193
D48V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               8               206
  CLUS_3              85               193
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q LOSS MUTATED       53     24      8
  4Q LOSS WILD-TYPE    123     66    108
D48V11, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              53               123
  CLUS_2              24                66
  CLUS_3               8               108
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q LOSS MUTATED       33     36     10      6
  4Q LOSS WILD-TYPE     68     64    136     29
D48V12, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              33                68
  CLUS_2              36                64
  CLUS_3              10               136
  CLUS_4               6                29

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED        1      4      0      0
  5P LOSS WILD-TYPE     13     13     12     10
D49V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED        1      0      4
  5P LOSS WILD-TYPE     18     19     11
D49V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               4                11
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P LOSS MUTATED        0      5     43      5      1      0
  5P LOSS WILD-TYPE    300     19    109     17     14      1
D49V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       35      7      3
  5P LOSS WILD-TYPE    117     81    157
D49V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              35               117
  CLUS_2               7                81
  CLUS_3               3               157
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5P LOSS MUTATED        5      6      0      1      0      3
  5P LOSS WILD-TYPE     36     31     39     11     41     21
D49V5, multiclass
D49V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5  10
  5P LOSS WILD-TYPE 116  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5   10
  5P LOSS WILD-TYPE  116   63
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5               116
  CLUS_2              10                63
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED       39      5      5      5
  5P LOSS WILD-TYPE    135     81    110    125
D49V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              39               135
  CLUS_2               5                81
  CLUS_3               5               110
  CLUS_4               5               125
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       48      1      5
  5P LOSS WILD-TYPE    191     83    177
D49V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              48               191
  CLUS_2               1                83
  CLUS_3               5               177
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5P LOSS MUTATED       33      5      5      4      7
  5P LOSS WILD-TYPE    116    133     44     49    109
D49V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED        1      6     47
  5P LOSS WILD-TYPE     12    208    231
D49V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               6               208
  CLUS_3              47               231
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5P LOSS MUTATED       30      9      5
  5P LOSS WILD-TYPE    146     81    111
D49V11, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              30               146
  CLUS_2               9                81
  CLUS_3               5               111
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5P LOSS MUTATED       16     20      5      3
  5P LOSS WILD-TYPE     85     80    141     32
D49V12, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              16                85
  CLUS_2              20                80
  CLUS_3               5               141
  CLUS_4               3                32

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        1      6      0      0
  5Q LOSS WILD-TYPE     13     11     12     10
D50V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               6                11
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        1      0      6
  5Q LOSS WILD-TYPE     18     19      9
D50V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               6                 9
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q LOSS MUTATED        0      5     61      5      1      0
  5Q LOSS WILD-TYPE    300     19     91     17     14      1
D50V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       49      8      3
  5Q LOSS WILD-TYPE    103     80    157
D50V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              49               103
  CLUS_2               8                80
  CLUS_3               3               157
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  5Q LOSS MUTATED        5      7      1      0      0      6
  5Q LOSS WILD-TYPE     36     30     38     12     41     18
D50V5, multiclass
D50V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     7  12
  5Q LOSS WILD-TYPE 114  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   12
  5Q LOSS WILD-TYPE  114   61
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7               114
  CLUS_2              12                61
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED       57      5      4      6
  5Q LOSS WILD-TYPE    117     81    111    124
D50V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              57               117
  CLUS_2               5                81
  CLUS_3               4               111
  CLUS_4               6               124
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       64      1      7
  5Q LOSS WILD-TYPE    175     83    175
D50V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              64               175
  CLUS_2               1                83
  CLUS_3               7               175
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q LOSS MUTATED       45      5      9      5      7
  5Q LOSS WILD-TYPE    104    133     40     48    109
D50V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        0      7     64
  5Q LOSS WILD-TYPE     13    207    214
D50V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               7               207
  CLUS_3              64               214
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED       40     13      5
  5Q LOSS WILD-TYPE    136     77    111
D50V11, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              40               136
  CLUS_2              13                77
  CLUS_3               5               111
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED       21     26      5      6
  5Q LOSS WILD-TYPE     80     74    141     29
D50V12, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              21                80
  CLUS_2              26                74
  CLUS_3               5               141
  CLUS_4               6                29

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        1      3      0      0
  6P LOSS WILD-TYPE     13     14     12     10
D51V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        1      0      3
  6P LOSS WILD-TYPE     18     19     12
D51V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               3                12
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P LOSS MUTATED        0      3     13      0      0      0
  6P LOSS WILD-TYPE    300     21    139     22     15      1
D51V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        7      3      0
  6P LOSS WILD-TYPE    145     85    160
D51V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               145
  CLUS_2               3                85
  CLUS_3               0               160
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6P LOSS MUTATED        1      3      0      0      1      0
  6P LOSS WILD-TYPE     40     34     39     12     40     24
D51V5, multiclass
D51V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2   3
  6P LOSS WILD-TYPE 119  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    3
  6P LOSS WILD-TYPE  119   70
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               3                70
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED       14      0      1      1
  6P LOSS WILD-TYPE    160     86    114    129
D51V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              14               160
  CLUS_2               0                86
  CLUS_3               1               114
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED       14      0      2
  6P LOSS WILD-TYPE    225     84    180
D51V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1              14               225
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6P LOSS MUTATED        9      1      1      2      1
  6P LOSS WILD-TYPE    140    137     48     51    115
D51V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        1      0     13
  6P LOSS WILD-TYPE     12    214    265
D51V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0               214
  CLUS_3              13               265
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6P LOSS MUTATED        7      3      1
  6P LOSS WILD-TYPE    169     87    115
D51V11, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7               169
  CLUS_2               3                87
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6P LOSS MUTATED        4      5      1      1
  6P LOSS WILD-TYPE     97     95    145     34
D51V12, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                97
  CLUS_2               5                95
  CLUS_3               1               145
  CLUS_4               1                34

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        1      3      0      0
  6Q LOSS WILD-TYPE     13     14     12     10
D52V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                14
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        1      0      3
  6Q LOSS WILD-TYPE     18     19     12
D52V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               3                12
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q LOSS MUTATED        0      3     20      0      0      0
  6Q LOSS WILD-TYPE    300     21    132     22     15      1
D52V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       13      4      0
  6Q LOSS WILD-TYPE    139     84    160
D52V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              13               139
  CLUS_2               4                84
  CLUS_3               0               160
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  6Q LOSS MUTATED        1      3      0      0      1      1
  6Q LOSS WILD-TYPE     40     34     39     12     40     23
D52V5, multiclass
D52V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3   3
  6Q LOSS WILD-TYPE 118  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3    3
  6Q LOSS WILD-TYPE  118   70
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3               118
  CLUS_2               3                70
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED       21      0      1      1
  6Q LOSS WILD-TYPE    153     86    114    129
D52V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              21               153
  CLUS_2               0                86
  CLUS_3               1               114
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       21      0      2
  6Q LOSS WILD-TYPE    218     84    180
D52V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              21               218
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  6Q LOSS MUTATED       13      1      3      3      1
  6Q LOSS WILD-TYPE    136    137     46     50    115
D52V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED        1      0     20
  6Q LOSS WILD-TYPE     12    214    258
D52V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0               214
  CLUS_3              20               258
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  6Q LOSS MUTATED       12      5      1
  6Q LOSS WILD-TYPE    164     85    115
D52V11, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12               164
  CLUS_2               5                85
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  6Q LOSS MUTATED        7      8      1      2
  6Q LOSS WILD-TYPE     94     92    145     33
D52V12, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                94
  CLUS_2               8                92
  CLUS_3               1               145
  CLUS_4               2                33

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        0      4      0      0
  7P LOSS WILD-TYPE     14     13     12     10
D53V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               4                13
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        0      0      4
  7P LOSS WILD-TYPE     19     19     11
D53V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               0                19
  CLUS_3               4                11
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P LOSS MUTATED        3      1     37      1      0      0
  7P LOSS WILD-TYPE    297     23    115     21     15      1
D53V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       23      9      5
  7P LOSS WILD-TYPE    129     79    155
D53V4, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              23               129
  CLUS_2               9                79
  CLUS_3               5               155
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7P LOSS MUTATED        3      4      0      1      0      0
  7P LOSS WILD-TYPE     38     33     39     11     41     24
D53V5, multiclass
D53V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   6
  7P LOSS WILD-TYPE 119  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    6
  7P LOSS WILD-TYPE  119   67
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               6                67
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED       35      1      3      3
  7P LOSS WILD-TYPE    139     85    112    127
D53V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              35               139
  CLUS_2               1                85
  CLUS_3               3               112
  CLUS_4               3               127
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       38      0      4
  7P LOSS WILD-TYPE    201     84    178
D53V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              38               201
  CLUS_2               0                84
  CLUS_3               4               178
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P LOSS MUTATED       27      6      5      2      2
  7P LOSS WILD-TYPE    122    132     44     51    114
D53V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED        2      7     33
  7P LOSS WILD-TYPE     11    207    245
D53V10, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               7               207
  CLUS_3              33               245
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       19     11      5
  7P LOSS WILD-TYPE    157     79    111
D53V11, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              19               157
  CLUS_2              11                79
  CLUS_3               5               111
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED       14     14      7      0
  7P LOSS WILD-TYPE     87     86    139     35
D53V12, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              14                87
  CLUS_2              14                86
  CLUS_3               7               139
  CLUS_4               0                35

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        0      1      0      0
  7Q LOSS WILD-TYPE     14     16     12     10
D54V1, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED        0      0      1
  7Q LOSS WILD-TYPE     19     19     14
D54V2, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q LOSS MUTATED        0      1     39      0      0      0
  7Q LOSS WILD-TYPE    300     23    113     22     15      1
D54V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       28      8      1
  7Q LOSS WILD-TYPE    124     80    159
D54V4, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              28               124
  CLUS_2               8                80
  CLUS_3               1               159
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  7Q LOSS MUTATED        4      4      0      0      0      2
  7Q LOSS WILD-TYPE     37     33     39     12     41     22
D54V5, multiclass
D54V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   9
  7Q LOSS WILD-TYPE 120  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    9
  7Q LOSS WILD-TYPE  120   64
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1               120
  CLUS_2               9                64
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED       38      1      0      1
  7Q LOSS WILD-TYPE    136     85    115    129
D54V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              38               136
  CLUS_2               1                85
  CLUS_3               0               115
  CLUS_4               1               129
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       38      0      2
  7Q LOSS WILD-TYPE    201     84    180
D54V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              38               201
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q LOSS MUTATED       32      2      4      1      1
  7Q LOSS WILD-TYPE    117    136     45     52    115
D54V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED        0      3     37
  7Q LOSS WILD-TYPE     13    211    241
D54V10, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               3               211
  CLUS_3              37               241
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       24      9      2
  7Q LOSS WILD-TYPE    152     81    114
D54V11, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              24               152
  CLUS_2               9                81
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED       13     19      2      1
  7Q LOSS WILD-TYPE     88     81    144     34
D54V12, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              13                88
  CLUS_2              19                81
  CLUS_3               2               144
  CLUS_4               1                34

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED        0      5      0      0
  8P LOSS WILD-TYPE     14     12     12     10
D55V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               5                12
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        0      0      5
  8P LOSS WILD-TYPE     19     19     10
D55V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               0                19
  CLUS_3               5                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P LOSS MUTATED        4      2     66      1      0      1
  8P LOSS WILD-TYPE    296     22     86     21     15      0
D55V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       51     12      2
  8P LOSS WILD-TYPE    101     76    158
D55V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              51               101
  CLUS_2              12                76
  CLUS_3               2               158
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8P LOSS MUTATED        5      2      3      0      0      5
  8P LOSS WILD-TYPE     36     35     36     12     41     19
D55V5, multiclass
D55V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     8   7
  8P LOSS WILD-TYPE 113  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8    7
  8P LOSS WILD-TYPE  113   66
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8               113
  CLUS_2               7                66
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED       60      8      2      3
  8P LOSS WILD-TYPE    114     78    113    127
D55V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              60               114
  CLUS_2               8                78
  CLUS_3               2               113
  CLUS_4               3               127
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       67      2      4
  8P LOSS WILD-TYPE    172     82    178
D55V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              67               172
  CLUS_2               2                82
  CLUS_3               4               178
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P LOSS MUTATED       54      4      6      2      5
  8P LOSS WILD-TYPE     95    134     43     51    111
D55V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED        2      5     64
  8P LOSS WILD-TYPE     11    209    214
D55V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               5               209
  CLUS_3              64               214
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P LOSS MUTATED       41     18      2
  8P LOSS WILD-TYPE    135     72    114
D55V11, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              41               135
  CLUS_2              18                72
  CLUS_3               2               114
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P LOSS MUTATED       22     31      5      3
  8P LOSS WILD-TYPE     79     69    141     32
D55V12, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              22                79
  CLUS_2              31                69
  CLUS_3               5               141
  CLUS_4               3                32

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        0      1      0      0
  8Q LOSS WILD-TYPE     14     16     12     10
D56V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      0      1
  8Q LOSS WILD-TYPE     19     19     14
D56V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q LOSS MUTATED        1      1     21      1      0      0
  8Q LOSS WILD-TYPE    299     23    131     21     15      1
D56V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       20      2      0
  8Q LOSS WILD-TYPE    132     86    160
D56V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              20               132
  CLUS_2               2                86
  CLUS_3               0               160
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  8Q LOSS MUTATED        0      2      1      0      0      0
  8Q LOSS WILD-TYPE     41     35     38     12     41     24
D56V5, multiclass
D56V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2   1
  8Q LOSS WILD-TYPE 119  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE  119   72
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2               119
  CLUS_2               1                72
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED       20      2      0      2
  8Q LOSS WILD-TYPE    154     84    115    128
D56V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              20               154
  CLUS_2               2                84
  CLUS_3               0               115
  CLUS_4               2               128
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       22      0      2
  8Q LOSS WILD-TYPE    217     84    180
D56V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              22               217
  CLUS_2               0                84
  CLUS_3               2               180
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q LOSS MUTATED       18      2      1      0      2
  8Q LOSS WILD-TYPE    131    136     48     53    114
D56V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED        0      2     21
  8Q LOSS WILD-TYPE     13    212    257
D56V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                13
  CLUS_2               2               212
  CLUS_3              21               257
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q LOSS MUTATED       18      2      1
  8Q LOSS WILD-TYPE    158     88    115
D56V11, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1              18               158
  CLUS_2               2                88
  CLUS_3               1               115
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q LOSS MUTATED        6     14      1      0
  8Q LOSS WILD-TYPE     95     86    145     35
D56V12, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               6                95
  CLUS_2              14                86
  CLUS_3               1               145
  CLUS_4               0                35

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED        1      8      0      0
  9P LOSS WILD-TYPE     13      9     12     10
D57V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               8                 9
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        1      0      8
  9P LOSS WILD-TYPE     18     19      7
D57V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               0                19
  CLUS_3               8                 7
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P LOSS MUTATED        2      8     84      6      0      0
  9P LOSS WILD-TYPE    298     16     68     16     15      1
D57V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       54     22      9
  9P LOSS WILD-TYPE     98     66    151
D57V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              54                98
  CLUS_2              22                66
  CLUS_3               9               151
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9P LOSS MUTATED        5     10      1      1      1      6
  9P LOSS WILD-TYPE     36     27     38     11     40     18
D57V5, multiclass
D57V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    11  13
  9P LOSS WILD-TYPE 110  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11   13
  9P LOSS WILD-TYPE  110   60
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11               110
  CLUS_2              13                60
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       76      5      6     13
  9P LOSS WILD-TYPE     98     81    109    117
D57V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              76                98
  CLUS_2               5                81
  CLUS_3               6               109
  CLUS_4              13               117
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       83      3     14
  9P LOSS WILD-TYPE    156     81    168
D57V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              83               156
  CLUS_2               3                81
  CLUS_3              14               168
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9P LOSS MUTATED       62     12     10      7      6
  9P LOSS WILD-TYPE     87    126     39     46    110
D57V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED        3     14     80
  9P LOSS WILD-TYPE     10    200    198
D57V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2              14               200
  CLUS_3              80               198
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9P LOSS MUTATED       50     20     14
  9P LOSS WILD-TYPE    126     70    102
D57V11, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              50               126
  CLUS_2              20                70
  CLUS_3              14               102
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9P LOSS MUTATED       24     37     17      6
  9P LOSS WILD-TYPE     77     63    129     29
D57V12, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              24                77
  CLUS_2              37                63
  CLUS_3              17               129
  CLUS_4               6                29

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED        0      9      0      0
  9Q LOSS WILD-TYPE     14      8     12     10
D58V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               9                 8
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        0      0      9
  9Q LOSS WILD-TYPE     19     19      6
D58V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               0                19
  CLUS_3               9                 6
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q LOSS MUTATED        4      7     97      9      0      0
  9Q LOSS WILD-TYPE    296     17     55     13     15      1
D58V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       63     25     13
  9Q LOSS WILD-TYPE     89     63    147
D58V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              63                89
  CLUS_2              25                63
  CLUS_3              13               147
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  9Q LOSS MUTATED        6     12      1      2      1      6
  9Q LOSS WILD-TYPE     35     25     38     10     40     18
D58V5, multiclass
D58V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    14  14
  9Q LOSS WILD-TYPE 107  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14   14
  9Q LOSS WILD-TYPE  107   59
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              14               107
  CLUS_2              14                59
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       86      7     10     14
  9Q LOSS WILD-TYPE     88     79    105    116
D58V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              86                88
  CLUS_2               7                79
  CLUS_3              10               105
  CLUS_4              14               116
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       97      4     16
  9Q LOSS WILD-TYPE    142     80    166
D58V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              97               142
  CLUS_2               4                80
  CLUS_3              16               166
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  9Q LOSS MUTATED       76     14     11      8      5
  9Q LOSS WILD-TYPE     73    124     38     45    111
D58V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED        4     18     92
  9Q LOSS WILD-TYPE      9    196    186
D58V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                 9
  CLUS_2              18               196
  CLUS_3              92               186
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  9Q LOSS MUTATED       58     25     16
  9Q LOSS WILD-TYPE    118     65    100
D58V11, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              58               118
  CLUS_2              25                65
  CLUS_3              16               100
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  9Q LOSS MUTATED       27     43     21      8
  9Q LOSS WILD-TYPE     74     57    125     27
D58V12, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              27                74
  CLUS_2              43                57
  CLUS_3              21               125
  CLUS_4               8                27

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED        0      4      0      0
  10P LOSS WILD-TYPE     14     13     12     10
D59V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        0      0      4
  10P LOSS WILD-TYPE     19     19     11
D59V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                4                 11
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P LOSS MUTATED        0      1     38      1      0      0
  10P LOSS WILD-TYPE    300     23    114     21     15      1
D59V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       24      9      1
  10P LOSS WILD-TYPE    128     79    159
D59V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               24                128
  CLUS_2                9                 79
  CLUS_3                1                159
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10P LOSS MUTATED        2      3      0      0      0      3
  10P LOSS WILD-TYPE     39     34     39     12     41     21
D59V5, multiclass
D59V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4   4
  10P LOSS WILD-TYPE 117  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    4
  10P LOSS WILD-TYPE  117   69
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                117
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED       33      3      1      3
  10P LOSS WILD-TYPE    141     83    114    127
D59V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               33                141
  CLUS_2                3                 83
  CLUS_3                1                114
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       36      1      3
  10P LOSS WILD-TYPE    203     83    179
D59V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               36                203
  CLUS_2                1                 83
  CLUS_3                3                179
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10P LOSS MUTATED       28      1      4      3      2
  10P LOSS WILD-TYPE    121    137     45     50    114
D59V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED        0      3     35
  10P LOSS WILD-TYPE     13    211    243
D59V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                3                211
  CLUS_3               35                243
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10P LOSS MUTATED       18     12      3
  10P LOSS WILD-TYPE    158     78    113
D59V11, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               18                158
  CLUS_2               12                 78
  CLUS_3                3                113
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10P LOSS MUTATED       13     16      3      1
  10P LOSS WILD-TYPE     88     84    143     34
D59V12, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               13                 88
  CLUS_2               16                 84
  CLUS_3                3                143
  CLUS_4                1                 34

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED        0      3      0      0
  10Q LOSS WILD-TYPE     14     14     12     10
D60V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        0      0      3
  10Q LOSS WILD-TYPE     19     19     12
D60V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q LOSS MUTATED        1      1     35      1      0      0
  10Q LOSS WILD-TYPE    299     23    117     21     15      1
D60V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       24      8      1
  10Q LOSS WILD-TYPE    128     80    159
D60V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               24                128
  CLUS_2                8                 80
  CLUS_3                1                159
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  10Q LOSS MUTATED        3      3      0      0      0      3
  10Q LOSS WILD-TYPE     38     34     39     12     41     21
D60V5, multiclass
D60V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5   4
  10Q LOSS WILD-TYPE 116  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    4
  10Q LOSS WILD-TYPE  116   69
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                116
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED       30      3      1      4
  10Q LOSS WILD-TYPE    144     83    114    126
D60V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               30                144
  CLUS_2                3                 83
  CLUS_3                1                114
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       33      1      4
  10Q LOSS WILD-TYPE    206     83    178
D60V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               33                206
  CLUS_2                1                 83
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q LOSS MUTATED       26      2      4      3      2
  10Q LOSS WILD-TYPE    123    136     45     50    114
D60V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED        0      4     33
  10Q LOSS WILD-TYPE     13    210    245
D60V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                210
  CLUS_3               33                245
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q LOSS MUTATED       20      8      4
  10Q LOSS WILD-TYPE    156     82    112
D60V11, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               20                156
  CLUS_2                8                 82
  CLUS_3                4                112
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q LOSS MUTATED       10     16      4      2
  10Q LOSS WILD-TYPE     91     84    142     33
D60V12, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               10                 91
  CLUS_2               16                 84
  CLUS_3                4                142
  CLUS_4                2                 33

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED        0      2      0      0
  11P LOSS WILD-TYPE     14     15     12     10
D61V1, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        0      0      2
  11P LOSS WILD-TYPE     19     19     13
D61V2, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P LOSS MUTATED        1      8     59      3      0      0
  11P LOSS WILD-TYPE    299     16     93     19     15      1
D61V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       45     16      5
  11P LOSS WILD-TYPE    107     72    155
D61V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               45                107
  CLUS_2               16                 72
  CLUS_3                5                155
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11P LOSS MUTATED        3      5      3      0      1      0
  11P LOSS WILD-TYPE     38     32     36     12     40     24
D61V5, multiclass
D61V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     6   6
  11P LOSS WILD-TYPE 115  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    6
  11P LOSS WILD-TYPE  115   67
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                115
  CLUS_2                6                 67
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED       53      7      5      6
  11P LOSS WILD-TYPE    121     79    110    124
D61V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               53                121
  CLUS_2                7                 79
  CLUS_3                5                110
  CLUS_4                6                124
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       61      1      9
  11P LOSS WILD-TYPE    178     83    173
D61V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               61                178
  CLUS_2                1                 83
  CLUS_3                9                173
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P LOSS MUTATED       46      8      7      6      3
  11P LOSS WILD-TYPE    103    130     42     47    113
D61V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED        1     10     59
  11P LOSS WILD-TYPE     12    204    219
D61V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2               10                204
  CLUS_3               59                219
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P LOSS MUTATED       43     14      9
  11P LOSS WILD-TYPE    133     76    107
D61V11, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               43                133
  CLUS_2               14                 76
  CLUS_3                9                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P LOSS MUTATED       17     35     11      3
  11P LOSS WILD-TYPE     84     65    135     32
D61V12, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               17                 84
  CLUS_2               35                 65
  CLUS_3               11                135
  CLUS_4                3                 32

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED        0      0      0      0
  11Q LOSS WILD-TYPE     14     17     12     10
D62V1, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        0      0      0
  11Q LOSS WILD-TYPE     19     19     15
D62V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q LOSS MUTATED        1      8     54      5      0      0
  11Q LOSS WILD-TYPE    299     16     98     17     15      1
D62V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       44     15      6
  11Q LOSS WILD-TYPE    108     73    154
D62V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               44                108
  CLUS_2               15                 73
  CLUS_3                6                154
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  11Q LOSS MUTATED        2      3      3      0      1      1
  11Q LOSS WILD-TYPE     39     34     36     12     40     23
D62V5, multiclass
D62V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6   4
  11Q LOSS WILD-TYPE 115  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6    4
  11Q LOSS WILD-TYPE  115   69
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                115
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED       50      6      4      8
  11Q LOSS WILD-TYPE    124     80    111    122
D62V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               50                124
  CLUS_2                6                 80
  CLUS_3                4                111
  CLUS_4                8                122
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       57      1     10
  11Q LOSS WILD-TYPE    182     83    172
D62V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               57                182
  CLUS_2                1                 83
  CLUS_3               10                172
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q LOSS MUTATED       46      9      4      6      3
  11Q LOSS WILD-TYPE    103    129     45     47    113
D62V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED        1     10     57
  11Q LOSS WILD-TYPE     12    204    221
D62V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2               10                204
  CLUS_3               57                221
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q LOSS MUTATED       45     10     10
  11Q LOSS WILD-TYPE    131     80    106
D62V11, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               45                131
  CLUS_2               10                 80
  CLUS_3               10                106
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q LOSS MUTATED       13     39     11      2
  11Q LOSS WILD-TYPE     88     61    135     33
D62V12, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               13                 88
  CLUS_2               39                 61
  CLUS_3               11                135
  CLUS_4                2                 33

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        0      3      0      0
  12P LOSS WILD-TYPE     14     14     12     10
D63V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED        0      0      3
  12P LOSS WILD-TYPE     19     19     12
D63V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P LOSS MUTATED        0      1     39      1      1      0
  12P LOSS WILD-TYPE    300     23    113     21     14      1
D63V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       24      7      4
  12P LOSS WILD-TYPE    128     81    156
D63V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               24                128
  CLUS_2                7                 81
  CLUS_3                4                156
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12P LOSS MUTATED        2      6      1      0      0      2
  12P LOSS WILD-TYPE     39     31     38     12     41     22
D63V5, multiclass
D63V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     4   7
  12P LOSS WILD-TYPE 117  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    7
  12P LOSS WILD-TYPE  117   66
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                117
  CLUS_2                7                 66
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED       35      0      2      5
  12P LOSS WILD-TYPE    139     86    113    125
D63V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               35                139
  CLUS_2                0                 86
  CLUS_3                2                113
  CLUS_4                5                125
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       35      1      6
  12P LOSS WILD-TYPE    204     83    176
D63V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               35                204
  CLUS_2                1                 83
  CLUS_3                6                176
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P LOSS MUTATED       28      4      4      1      3
  12P LOSS WILD-TYPE    121    134     45     52    113
D63V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED        0      5     35
  12P LOSS WILD-TYPE     13    209    243
D63V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                5                209
  CLUS_3               35                243
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED       27      4      4
  12P LOSS WILD-TYPE    149     86    112
D63V11, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1               27                149
  CLUS_2                4                 86
  CLUS_3                4                112
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        8     19      5      3
  12P LOSS WILD-TYPE     93     81    141     32
D63V12, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                8                 93
  CLUS_2               19                 81
  CLUS_3                5                141
  CLUS_4                3                 32

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED        0      2      0      0
  12Q LOSS WILD-TYPE     14     15     12     10
D64V1, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A053         TCGA-AP-A054 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED        0      0      2
  12Q LOSS WILD-TYPE     19     19     13
D64V2, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A053         TCGA-AP-A054 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q LOSS MUTATED        0      1     32      1      1      0
  12Q LOSS WILD-TYPE    300     23    120     21     14      1
D64V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       22      5      2
  12Q LOSS WILD-TYPE    130     83    158
D64V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               22                130
  CLUS_2                5                 83
  CLUS_3                2                158
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  12Q LOSS MUTATED        2      5      1      0      0      2
  12Q LOSS WILD-TYPE     39     32     38     12     41     22
D64V5, multiclass
D64V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   7
  12Q LOSS WILD-TYPE 118  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    7
  12Q LOSS WILD-TYPE  118   66
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                3                118
  CLUS_2                7                 66
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED       31      0      1      3
  12Q LOSS WILD-TYPE    143     86    114    127
D64V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               31                143
  CLUS_2                0                 86
  CLUS_3                1                114
  CLUS_4                3                127
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       31      0      4
  12Q LOSS WILD-TYPE    208     84    178
D64V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               31                208
  CLUS_2                0                 84
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12Q LOSS MUTATED       21      2      5      2      3
  12Q LOSS WILD-TYPE    128    136     44     51    113
D64V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED        0      2     31
  12Q LOSS WILD-TYPE     13    212    247
D64V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                212
  CLUS_3               31                247
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12Q LOSS MUTATED       23      4      2
  12Q LOSS WILD-TYPE    153     86    114
D64V11, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1               23                153
  CLUS_2                4                 86
  CLUS_3                2                114
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12Q LOSS MUTATED        8     16      2      3
  12Q LOSS WILD-TYPE     93     84    144     32
D64V12, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                8                 93
  CLUS_2               16                 84
  CLUS_3                2                144
  CLUS_4                3                 32

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED        1      2      1      0
  13Q LOSS WILD-TYPE     13     15     11     10
D65V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 15
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        1      1      2
  13Q LOSS WILD-TYPE     18     18     13
D65V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                1                 18
  CLUS_3                2                 13
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q LOSS MUTATED        5      8     63      9      1      0
  13Q LOSS WILD-TYPE    295     16     89     13     14      1
D65V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       44     18     12
  13Q LOSS WILD-TYPE    108     70    148
D65V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               44                108
  CLUS_2               18                 70
  CLUS_3               12                148
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  13Q LOSS MUTATED        4      8      0      1      3      4
  13Q LOSS WILD-TYPE     37     29     39     11     38     20
D65V5, multiclass
D65V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9  11
  13Q LOSS WILD-TYPE 112  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   11
  13Q LOSS WILD-TYPE  112   62
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                112
  CLUS_2               11                 62
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED       55      5     12     14
  13Q LOSS WILD-TYPE    119     81    103    116
D65V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               55                119
  CLUS_2                5                 81
  CLUS_3               12                103
  CLUS_4               14                116
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       65      1     20
  13Q LOSS WILD-TYPE    174     83    162
D65V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               65                174
  CLUS_2                1                 83
  CLUS_3               20                162
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q LOSS MUTATED       46     14      6     13      6
  13Q LOSS WILD-TYPE    103    124     43     40    110
D65V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED        5     16     64
  13Q LOSS WILD-TYPE      8    198    214
D65V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                5                  8
  CLUS_2               16                198
  CLUS_3               64                214
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q LOSS MUTATED       44     13     18
  13Q LOSS WILD-TYPE    132     77     98
D65V11, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               44                132
  CLUS_2               13                 77
  CLUS_3               18                 98
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q LOSS MUTATED       19     30     20      6
  13Q LOSS WILD-TYPE     82     70    126     29
D65V12, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               19                 82
  CLUS_2               30                 70
  CLUS_3               20                126
  CLUS_4                6                 29

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED        0      6      0      0
  14Q LOSS WILD-TYPE     14     11     12     10
D66V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED        0      0      6
  14Q LOSS WILD-TYPE     19     19      9
D66V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                6                  9
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q LOSS MUTATED        0      5     51      2      1      0
  14Q LOSS WILD-TYPE    300     19    101     20     14      1
D66V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       37      8      1
  14Q LOSS WILD-TYPE    115     80    159
D66V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               37                115
  CLUS_2                8                 80
  CLUS_3                1                159
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  14Q LOSS MUTATED        5      6      0      0      1      4
  14Q LOSS WILD-TYPE     36     31     39     12     40     20
D66V5, multiclass
D66V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4  12
  14Q LOSS WILD-TYPE 117  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4   12
  14Q LOSS WILD-TYPE  117   61
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                117
  CLUS_2               12                 61
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED       51      2      2      4
  14Q LOSS WILD-TYPE    123     84    113    126
D66V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               51                123
  CLUS_2                2                 84
  CLUS_3                2                113
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       53      0      6
  14Q LOSS WILD-TYPE    186     84    176
D66V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               53                186
  CLUS_2                0                 84
  CLUS_3                6                176
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  14Q LOSS MUTATED       37      2      4      7      7
  14Q LOSS WILD-TYPE    112    136     45     46    109
D66V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED        1      1     55
  14Q LOSS WILD-TYPE     12    213    223
D66V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                213
  CLUS_3               55                223
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  14Q LOSS MUTATED       35      9      3
  14Q LOSS WILD-TYPE    141     81    113
D66V11, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               35                141
  CLUS_2                9                 81
  CLUS_3                3                113
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  14Q LOSS MUTATED       14     24      4      5
  14Q LOSS WILD-TYPE     87     76    142     30
D66V12, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               14                 87
  CLUS_2               24                 76
  CLUS_3                4                142
  CLUS_4                5                 30

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      7      0      0
  15Q LOSS WILD-TYPE     14     10     12     10
D67V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                7                 10
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        0      0      7
  15Q LOSS WILD-TYPE     19     19      8
D67V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                7                  8
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q LOSS MUTATED        4      5     85      8      0      0
  15Q LOSS WILD-TYPE    296     19     67     14     15      1
D67V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED       61     21      7
  15Q LOSS WILD-TYPE     91     67    153
D67V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               61                 91
  CLUS_2               21                 67
  CLUS_3                7                153
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  15Q LOSS MUTATED        1     11      2      1      1      3
  15Q LOSS WILD-TYPE     40     26     37     11     40     21
D67V5, multiclass
D67V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     9  10
  15Q LOSS WILD-TYPE 112  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      9   10
  15Q LOSS WILD-TYPE  112   63
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                9                112
  CLUS_2               10                 63
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED       81      5     10      6
  15Q LOSS WILD-TYPE     93     81    105    124
D67V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               81                 93
  CLUS_2                5                 81
  CLUS_3               10                105
  CLUS_4                6                124
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED       91      2      9
  15Q LOSS WILD-TYPE    148     82    173
D67V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               91                148
  CLUS_2                2                 82
  CLUS_3                9                173
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q LOSS MUTATED       68      8     11      8      5
  15Q LOSS WILD-TYPE     81    130     38     45    111
D67V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        4      9     87
  15Q LOSS WILD-TYPE      9    205    191
D67V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                9                205
  CLUS_3               87                191
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED       61     18      9
  15Q LOSS WILD-TYPE    115     72    107
D67V11, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               61                115
  CLUS_2               18                 72
  CLUS_3                9                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED       24     45     13      6
  15Q LOSS WILD-TYPE     77     55    133     29
D67V12, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               24                 77
  CLUS_2               45                 55
  CLUS_3               13                133
  CLUS_4                6                 29

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED        0      6      0      0
  16P LOSS WILD-TYPE     14     11     12     10
D68V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED        0      0      6
  16P LOSS WILD-TYPE     19     19      9
D68V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                6                  9
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P LOSS MUTATED        5      5     79      3      1      0
  16P LOSS WILD-TYPE    295     19     73     19     14      1
D68V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       54     23      6
  16P LOSS WILD-TYPE     98     65    154
D68V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               54                 98
  CLUS_2               23                 65
  CLUS_3                6                154
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16P LOSS MUTATED        8      7      2      0      2      2
  16P LOSS WILD-TYPE     33     30     37     12     39     22
D68V5, multiclass
D68V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    10  11
  16P LOSS WILD-TYPE 111  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     10   11
  16P LOSS WILD-TYPE  111   62
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               10                111
  CLUS_2               11                 62
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED       73      5      8      7
  16P LOSS WILD-TYPE    101     81    107    123
D68V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               73                101
  CLUS_2                5                 81
  CLUS_3                8                107
  CLUS_4                7                123
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       80      2     11
  16P LOSS WILD-TYPE    159     82    171
D68V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               80                159
  CLUS_2                2                 82
  CLUS_3               11                171
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16P LOSS MUTATED       58     10     10      6      6
  16P LOSS WILD-TYPE     91    128     39     47    110
D68V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED        2     11     77
  16P LOSS WILD-TYPE     11    203    201
D68V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2               11                203
  CLUS_3               77                201
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16P LOSS MUTATED       49     24      9
  16P LOSS WILD-TYPE    127     66    107
D68V11, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               49                127
  CLUS_2               24                 66
  CLUS_3                9                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16P LOSS MUTATED       29     35     11      7
  16P LOSS WILD-TYPE     72     65    135     28
D68V12, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1               29                 72
  CLUS_2               35                 65
  CLUS_3               11                135
  CLUS_4                7                 28

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      8      1      0
  16Q LOSS WILD-TYPE     14      9     11     10
D69V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                8                  9
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        0      1      8
  16Q LOSS WILD-TYPE     19     18      7
D69V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                1                 18
  CLUS_3                8                  7
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q LOSS MUTATED       15      8    106      4      1      0
  16Q LOSS WILD-TYPE    285     16     46     18     14      1
D69V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED       73     29     15
  16Q LOSS WILD-TYPE     79     59    145
D69V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               73                 79
  CLUS_2               29                 59
  CLUS_3               15                145
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  16Q LOSS MUTATED        7     10      3      1      6      4
  16Q LOSS WILD-TYPE     34     27     36     11     35     20
D69V5, multiclass
D69V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    19  12
  16Q LOSS WILD-TYPE 102  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     19   12
  16Q LOSS WILD-TYPE  102   61
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               19                102
  CLUS_2               12                 61
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED       97      9     15     13
  16Q LOSS WILD-TYPE     77     77    100    117
D69V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               97                 77
  CLUS_2                9                 77
  CLUS_3               15                100
  CLUS_4               13                117
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED      108      6     20
  16Q LOSS WILD-TYPE    131     78    162
D69V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1              108                131
  CLUS_2                6                 78
  CLUS_3               20                162
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q LOSS MUTATED       79     14     14     11     12
  16Q LOSS WILD-TYPE     70    124     35     42    104
D69V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        3     23    104
  16Q LOSS WILD-TYPE     10    191    174
D69V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2               23                191
  CLUS_3              104                174
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED       70     30     15
  16Q LOSS WILD-TYPE    106     60    101
D69V11, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               70                106
  CLUS_2               30                 60
  CLUS_3               15                101
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED       37     50     21      7
  16Q LOSS WILD-TYPE     64     50    125     28
D69V12, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               37                 64
  CLUS_2               50                 50
  CLUS_3               21                125
  CLUS_4                7                 28

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        0      7      1      0
  17P LOSS WILD-TYPE     14     10     11     10
D70V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                7                 10
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        1      0      7
  17P LOSS WILD-TYPE     18     19      8
D70V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 19
  CLUS_3                7                  8
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P LOSS MUTATED        2      4    107      7      0      0
  17P LOSS WILD-TYPE    298     20     45     15     15      1
D70V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED       71     23     11
  17P LOSS WILD-TYPE     81     65    149
D70V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               71                 81
  CLUS_2               23                 65
  CLUS_3               11                149
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17P LOSS MUTATED        5      8      3      0      1      8
  17P LOSS WILD-TYPE     36     29     36     12     40     16
D70V5, multiclass
D70V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    15  10
  17P LOSS WILD-TYPE 106  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     15   10
  17P LOSS WILD-TYPE  106   63
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               15                106
  CLUS_2               10                 63
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED       91      8      6     13
  17P LOSS WILD-TYPE     83     78    109    117
D70V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               91                 83
  CLUS_2                8                 78
  CLUS_3                6                109
  CLUS_4               13                117
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED       98      3     17
  17P LOSS WILD-TYPE    141     81    165
D70V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               98                141
  CLUS_2                3                 81
  CLUS_3               17                165
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P LOSS MUTATED       77     15     11      7      7
  17P LOSS WILD-TYPE     72    123     38     46    109
D70V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        3     20     94
  17P LOSS WILD-TYPE     10    194    184
D70V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2               20                194
  CLUS_3               94                184
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED       61     24     17
  17P LOSS WILD-TYPE    115     66     99
D70V11, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               61                115
  CLUS_2               24                 66
  CLUS_3               17                 99
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED       30     44     21      7
  17P LOSS WILD-TYPE     71     56    125     28
D70V12, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               30                 71
  CLUS_2               44                 56
  CLUS_3               21                125
  CLUS_4                7                 28

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        0      6      0      0
  17Q LOSS WILD-TYPE     14     11     12     10
D71V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        0      0      6
  17Q LOSS WILD-TYPE     19     19      9
D71V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                6                  9
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q LOSS MUTATED        1      3     75      7      0      0
  17Q LOSS WILD-TYPE    299     21     77     15     15      1
D71V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED       45     20     10
  17Q LOSS WILD-TYPE    107     68    150
D71V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               45                107
  CLUS_2               20                 68
  CLUS_3               10                150
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  17Q LOSS MUTATED        3      7      3      0      1      4
  17Q LOSS WILD-TYPE     38     30     36     12     40     20
D71V5, multiclass
D71V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    10   8
  17Q LOSS WILD-TYPE 111  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    8
  17Q LOSS WILD-TYPE  111   65
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               10                111
  CLUS_2                8                 65
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED       63      5      5     11
  17Q LOSS WILD-TYPE    111     81    110    119
D71V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               63                111
  CLUS_2                5                 81
  CLUS_3                5                110
  CLUS_4               11                119
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED       66      3     15
  17Q LOSS WILD-TYPE    173     81    167
D71V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               66                173
  CLUS_2                3                 81
  CLUS_3               15                167
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED       51     12      7      7      6
  17Q LOSS WILD-TYPE     98    126     42     46    110
D71V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        3     16     64
  17Q LOSS WILD-TYPE     10    198    214
D71V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2               16                198
  CLUS_3               64                214
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED       45     14     15
  17Q LOSS WILD-TYPE    131     76    101
D71V11, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               45                131
  CLUS_2               14                 76
  CLUS_3               15                101
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED       17     32     19      6
  17Q LOSS WILD-TYPE     84     68    127     29
D71V12, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1               17                 84
  CLUS_2               32                 68
  CLUS_3               19                127
  CLUS_4                6                 29

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        0      1      1      0
  18P LOSS WILD-TYPE     14     16     11     10
D72V1, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      0      1
  18P LOSS WILD-TYPE     18     19     14
D72V2, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P LOSS MUTATED        1      5     38      8      0      0
  18P LOSS WILD-TYPE    299     19    114     14     15      1
D72V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       33      9      4
  18P LOSS WILD-TYPE    119     79    156
D72V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               33                119
  CLUS_2                9                 79
  CLUS_3                4                156
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18P LOSS MUTATED        1      4      2      0      2      3
  18P LOSS WILD-TYPE     40     33     37     12     39     21
D72V5, multiclass
D72V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     8   4
  18P LOSS WILD-TYPE 113  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8    4
  18P LOSS WILD-TYPE  113   69
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                8                113
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED       35      5      6      6
  18P LOSS WILD-TYPE    139     81    109    124
D72V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               35                139
  CLUS_2                5                 81
  CLUS_3                6                109
  CLUS_4                6                124
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       41      2      9
  18P LOSS WILD-TYPE    198     82    173
D72V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               41                198
  CLUS_2                2                 82
  CLUS_3                9                173
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P LOSS MUTATED       31      7      4      6      3
  18P LOSS WILD-TYPE    118    131     45     47    113
D72V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        1      8     42
  18P LOSS WILD-TYPE     12    206    236
D72V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                8                206
  CLUS_3               42                236
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED       32      7      7
  18P LOSS WILD-TYPE    144     83    109
D72V11, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               32                144
  CLUS_2                7                 83
  CLUS_3                7                109
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        9     20     10      7
  18P LOSS WILD-TYPE     92     80    136     28
D72V12, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                9                 92
  CLUS_2               20                 80
  CLUS_3               10                136
  CLUS_4                7                 28

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        0      2      1      0
  18Q LOSS WILD-TYPE     14     15     11     10
D73V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 15
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        1      0      2
  18Q LOSS WILD-TYPE     18     19     13
D73V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 19
  CLUS_3                2                 13
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q LOSS MUTATED        1      5     49     10      0      0
  18Q LOSS WILD-TYPE    299     19    103     12     15      1
D73V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       41     12      6
  18Q LOSS WILD-TYPE    111     76    154
D73V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               41                111
  CLUS_2               12                 76
  CLUS_3                6                154
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  18Q LOSS MUTATED        4      4      2      1      1      3
  18Q LOSS WILD-TYPE     37     33     37     11     40     21
D73V5, multiclass
D73V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     9   6
  18Q LOSS WILD-TYPE 112  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9    6
  18Q LOSS WILD-TYPE  112   67
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                112
  CLUS_2                6                 67
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED       44      8      6      7
  18Q LOSS WILD-TYPE    130     78    109    123
D73V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               44                130
  CLUS_2                8                 78
  CLUS_3                6                109
  CLUS_4                7                123
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       54      1     10
  18Q LOSS WILD-TYPE    185     83    172
D73V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               54                185
  CLUS_2                1                 83
  CLUS_3               10                172
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q LOSS MUTATED       39      9      6      5      5
  18Q LOSS WILD-TYPE    110    129     43     48    111
D73V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        2      8     54
  18Q LOSS WILD-TYPE     11    206    224
D73V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                8                206
  CLUS_3               54                224
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED       39     11      9
  18Q LOSS WILD-TYPE    137     79    107
D73V11, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               39                137
  CLUS_2               11                 79
  CLUS_3                9                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED       15     25     12      7
  18Q LOSS WILD-TYPE     86     75    134     28
D73V12, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               15                 86
  CLUS_2               25                 75
  CLUS_3               12                134
  CLUS_4                7                 28

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        0      2      0      0
  19P LOSS WILD-TYPE     14     15     12     10
D74V1, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        0      0      2
  19P LOSS WILD-TYPE     19     19     13
D74V2, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P LOSS MUTATED        1      7     42      7      0      0
  19P LOSS WILD-TYPE    299     17    110     15     15      1
D74V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       42      7      2
  19P LOSS WILD-TYPE    110     81    158
D74V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               42                110
  CLUS_2                7                 81
  CLUS_3                2                158
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19P LOSS MUTATED        3      4      1      0      1      5
  19P LOSS WILD-TYPE     38     33     38     12     40     19
D74V5, multiclass
D74V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     7   7
  19P LOSS WILD-TYPE 114  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7    7
  19P LOSS WILD-TYPE  114   66
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                7                114
  CLUS_2                7                 66
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED       42      7      4      4
  19P LOSS WILD-TYPE    132     79    111    126
D74V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               42                132
  CLUS_2                7                 79
  CLUS_3                4                111
  CLUS_4                4                126
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       50      1      6
  19P LOSS WILD-TYPE    189     83    176
D74V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               50                189
  CLUS_2                1                 83
  CLUS_3                6                176
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P LOSS MUTATED       38      5      3      4      5
  19P LOSS WILD-TYPE    111    133     46     49    111
D74V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        2      6     47
  19P LOSS WILD-TYPE     11    208    231
D74V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                6                208
  CLUS_3               47                231
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED       38      7      5
  19P LOSS WILD-TYPE    138     83    111
D74V11, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               38                138
  CLUS_2                7                 83
  CLUS_3                5                111
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED       10     30      5      5
  19P LOSS WILD-TYPE     91     70    141     30
D74V12, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               10                 91
  CLUS_2               30                 70
  CLUS_3                5                141
  CLUS_4                5                 30

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        0      3      1      0
  19Q LOSS WILD-TYPE     14     14     11     10
D75V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                3                 14
  CLUS_3                1                 11
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED        1      0      3
  19Q LOSS WILD-TYPE     18     19     12
D75V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 19
  CLUS_3                3                 12
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q LOSS MUTATED        2      6     39      5      0      0
  19Q LOSS WILD-TYPE    298     18    113     17     15      1
D75V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       32      9      4
  19Q LOSS WILD-TYPE    120     79    156
D75V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               32                120
  CLUS_2                9                 79
  CLUS_3                4                156
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  19Q LOSS MUTATED        3      4      1      0      1      4
  19Q LOSS WILD-TYPE     38     33     38     12     40     20
D75V5, multiclass
D75V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     7   6
  19Q LOSS WILD-TYPE 114  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7    6
  19Q LOSS WILD-TYPE  114   67
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                7                114
  CLUS_2                6                 67
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       36      6      4      5
  19Q LOSS WILD-TYPE    138     80    111    125
D75V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               36                138
  CLUS_2                6                 80
  CLUS_3                4                111
  CLUS_4                5                125
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       43      1      7
  19Q LOSS WILD-TYPE    196     83    175
D75V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               43                196
  CLUS_2                1                 83
  CLUS_3                7                175
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q LOSS MUTATED       32      6      3      4      5
  19Q LOSS WILD-TYPE    117    132     46     49    111
D75V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED        3      7     40
  19Q LOSS WILD-TYPE     10    207    238
D75V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                7                207
  CLUS_3               40                238
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED       31      7      6
  19Q LOSS WILD-TYPE    145     83    110
D75V11, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               31                145
  CLUS_2                7                 83
  CLUS_3                6                110
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED       10     24      6      4
  19Q LOSS WILD-TYPE     91     76    140     31
D75V12, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               10                 91
  CLUS_2               24                 76
  CLUS_3                6                140
  CLUS_4                4                 31

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED        1      0      0      0
  20P LOSS WILD-TYPE     13     17     12     10
D76V1, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        1      0      0
  20P LOSS WILD-TYPE     18     19     15
D76V2, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P LOSS MUTATED        1      3     13      1      0      0
  20P LOSS WILD-TYPE    299     21    139     21     15      1
D76V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        7      3      2
  20P LOSS WILD-TYPE    145     85    158
D76V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                145
  CLUS_2                3                 85
  CLUS_3                2                158
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20P LOSS MUTATED        1      2      0      0      1      1
  20P LOSS WILD-TYPE     40     35     39     12     40     23
D76V5, multiclass
D76V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   4
  20P LOSS WILD-TYPE 120  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    4
  20P LOSS WILD-TYPE  120   69
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                120
  CLUS_2                4                 69
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED       11      2      2      2
  20P LOSS WILD-TYPE    163     84    113    128
D76V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               11                163
  CLUS_2                2                 84
  CLUS_3                2                113
  CLUS_4                2                128
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED       13      0      4
  20P LOSS WILD-TYPE    226     84    178
D76V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1               13                226
  CLUS_2                0                 84
  CLUS_3                4                178
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20P LOSS MUTATED        9      1      2      2      4
  20P LOSS WILD-TYPE    140    137     47     51    112
D76V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        1      2     15
  20P LOSS WILD-TYPE     12    212    263
D76V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                212
  CLUS_3               15                263
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20P LOSS MUTATED        7      4      2
  20P LOSS WILD-TYPE    169     86    114
D76V11, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                7                169
  CLUS_2                4                 86
  CLUS_3                2                114
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20P LOSS MUTATED        5      4      2      2
  20P LOSS WILD-TYPE     96     96    144     33
D76V12, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                5                 96
  CLUS_2                4                 96
  CLUS_3                2                144
  CLUS_4                2                 33

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        1      0      0      0
  20Q LOSS WILD-TYPE     13     17     12     10
D77V1, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        1      0      0
  20Q LOSS WILD-TYPE     18     19     15
D77V2, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q LOSS MUTATED        0      3      7      0      0      0
  20Q LOSS WILD-TYPE    300     21    145     22     15      1
D77V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        4      3      0
  20Q LOSS WILD-TYPE    148     85    160
D77V4, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                4                148
  CLUS_2                3                 85
  CLUS_3                0                160
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  20Q LOSS MUTATED        0      2      1      0      1      0
  20Q LOSS WILD-TYPE     41     35     38     12     40     24
D77V5, multiclass
D77V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   2
  20Q LOSS WILD-TYPE 119  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    2
  20Q LOSS WILD-TYPE  119   71
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                2                119
  CLUS_2                2                 71
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        6      2      1      0
  20Q LOSS WILD-TYPE    168     84    114    130
D77V7, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                6                168
  CLUS_2                2                 84
  CLUS_3                1                114
  CLUS_4                0                130
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        8      0      1
  20Q LOSS WILD-TYPE    231     84    181
D77V8, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                8                231
  CLUS_2                0                 84
  CLUS_3                1                181
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  20Q LOSS MUTATED        4      0      2      2      2
  20Q LOSS WILD-TYPE    145    138     47     51    114
D77V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        1      0      9
  20Q LOSS WILD-TYPE     12    214    269
D77V10, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                214
  CLUS_3                9                269
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  20Q LOSS MUTATED        5      2      0
  20Q LOSS WILD-TYPE    171     88    116
D77V11, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                5                171
  CLUS_2                2                 88
  CLUS_3                0                116
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  20Q LOSS MUTATED        3      3      0      1
  20Q LOSS WILD-TYPE     98     97    146     34
D77V12, multiclass
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CLUS_1                3                 98
  CLUS_2                3                 97
  CLUS_3                0                146
  CLUS_4                1                 34

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED        0      4      0      0
  21Q LOSS WILD-TYPE     14     13     12     10
D78V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                4                 13
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        0      0      4
  21Q LOSS WILD-TYPE     19     19     11
D78V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                4                 11
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q LOSS MUTATED        4      5     39      3      0      0
  21Q LOSS WILD-TYPE    296     19    113     19     15      1
D78V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       30      9      4
  21Q LOSS WILD-TYPE    122     79    156
D78V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               30                122
  CLUS_2                9                 79
  CLUS_3                4                156
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  21Q LOSS MUTATED        3      5      1      0      1      3
  21Q LOSS WILD-TYPE     38     32     38     12     40     21
D78V5, multiclass
D78V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6   7
  21Q LOSS WILD-TYPE 115  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6    7
  21Q LOSS WILD-TYPE  115   66
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                6                115
  CLUS_2                7                 66
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED       38      8      4      1
  21Q LOSS WILD-TYPE    136     78    111    129
D78V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               38                136
  CLUS_2                8                 78
  CLUS_3                4                111
  CLUS_4                1                129
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       43      5      3
  21Q LOSS WILD-TYPE    196     79    179
D78V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               43                196
  CLUS_2                5                 79
  CLUS_3                3                179
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q LOSS MUTATED       33      1      3      4      8
  21Q LOSS WILD-TYPE    116    137     46     49    108
D78V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED        0      4     45
  21Q LOSS WILD-TYPE     13    210    233
D78V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                4                210
  CLUS_3               45                233
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q LOSS MUTATED       33      9      1
  21Q LOSS WILD-TYPE    143     81    115
D78V11, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               33                143
  CLUS_2                9                 81
  CLUS_3                1                115
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q LOSS MUTATED       15     23      2      3
  21Q LOSS WILD-TYPE     86     77    144     32
D78V12, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               15                 86
  CLUS_2               23                 77
  CLUS_3                2                144
  CLUS_4                3                 32

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED        0      6      0      0
  22Q LOSS WILD-TYPE     14     11     12     10
D79V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                6                 11
  CLUS_3                0                 12
  CLUS_4                0                 10
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED        0      0      6
  22Q LOSS WILD-TYPE     19     19      9
D79V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 19
  CLUS_3                6                  9
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q LOSS MUTATED        3      5     89      8      0      0
  22Q LOSS WILD-TYPE    297     19     63     14     15      1
D79V3, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       59     24     13
  22Q LOSS WILD-TYPE     93     64    147
D79V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               59                 93
  CLUS_2               24                 64
  CLUS_3               13                147
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  22Q LOSS MUTATED        4      8      2      1      1      5
  22Q LOSS WILD-TYPE     37     29     37     11     40     19
D79V5, multiclass
D79V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    14   7
  22Q LOSS WILD-TYPE 107  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     14    7
  22Q LOSS WILD-TYPE  107   66
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               14                107
  CLUS_2                7                 66
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED       76      5      8     15
  22Q LOSS WILD-TYPE     98     81    107    115
D79V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               76                 98
  CLUS_2                5                 81
  CLUS_3                8                107
  CLUS_4               15                115
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       85      1     18
  22Q LOSS WILD-TYPE    154     83    164
D79V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               85                154
  CLUS_2                1                 83
  CLUS_3               18                164
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q LOSS MUTATED       65     17     10      8      3
  22Q LOSS WILD-TYPE     84    121     39     45    113
D79V9, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED        5     18     80
  22Q LOSS WILD-TYPE      8    196    198
D79V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                  8
  CLUS_2               18                196
  CLUS_3               80                198
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q LOSS MUTATED       52     23     17
  22Q LOSS WILD-TYPE    124     67     99
D79V11, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               52                124
  CLUS_2               23                 67
  CLUS_3               17                 99
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q LOSS MUTATED       27     40     20      5
  22Q LOSS WILD-TYPE     74     60    126     30
D79V12, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               27                 74
  CLUS_2               40                 60
  CLUS_3               20                126
  CLUS_4                5                 30

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        0      5      0      0
  XQ LOSS WILD-TYPE     14     12     12     10
D80V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               5                12
  CLUS_3               0                12
  CLUS_4               0                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        0      0      5
  XQ LOSS WILD-TYPE     19     19     10
D80V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               0                19
  CLUS_3               5                10
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ LOSS MUTATED        1      3     60      5      0      0
  XQ LOSS WILD-TYPE    299     21     92     17     15      1
D80V3, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       37     15      6
  XQ LOSS WILD-TYPE    115     73    154
D80V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              37               115
  CLUS_2              15                73
  CLUS_3               6               154
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
  XQ LOSS MUTATED        3     13      2      1      1      1
  XQ LOSS WILD-TYPE     38     24     37     11     40     23
D80V5, multiclass
D80V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     9  12
  XQ LOSS WILD-TYPE 112  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      9   12
  XQ LOSS WILD-TYPE  112   61
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               9               112
  CLUS_2              12                61
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED       54      4      6      4
  XQ LOSS WILD-TYPE    120     82    109    126
D80V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              54               120
  CLUS_2               4                82
  CLUS_3               6               109
  CLUS_4               4               126
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       59      1      8
  XQ LOSS WILD-TYPE    180     83    174
D80V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              59               180
  CLUS_2               1                83
  CLUS_3               8               174
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED       45      7      3      5      6
  XQ LOSS WILD-TYPE    104    131     46     48    110
D80V9, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        4      8     54
  XQ LOSS WILD-TYPE      9    206    224
D80V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                 9
  CLUS_2               8               206
  CLUS_3              54               224
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED       40     10      8
  XQ LOSS WILD-TYPE    136     80    108
D80V11, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              40               136
  CLUS_2              10                80
  CLUS_3               8               108
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED       14     30      8      6
  XQ LOSS WILD-TYPE     87     70    138     29
D80V12, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1              14                87
  CLUS_2              30                70
  CLUS_3               8               138
  CLUS_4               6                29
> q(save="no")
