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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/376256/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LGG-TP/2909315/1.GDAC_mergedClustering.Finished/LGG-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LGG-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oT=LGG-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=222, in cluster file=220, common to both=220
[1] "Reduce the number of clustering variables from 80 to 51."
[1]  51 220
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               214 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6               214 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8               212 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8               212 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               216 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               216 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               37               183 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               37               183 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               51               169 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               51               169 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14               206 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               14               206 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17               203 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17               203 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               216 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4               216 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6               214 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6               214 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                21                199 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                21                199 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                211 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                211 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                206 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                206 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                209 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                209 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                215 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                215 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                216 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                216 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                209 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                209 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                211 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                211 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                203 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                203 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                204 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                204 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                217 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                217 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               67               153 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               67               153 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               211 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               211 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               216 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               216 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               217 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3               217 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4               216 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4               216 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               211 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               211 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               15               205 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               15               205 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               24               196 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               24               196 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               209 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               209 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9               211 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9               211 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7               213 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7               213 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21               199 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21               199 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3               217 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3               217 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38               182 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38               182 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6               214 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6               214 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                31                189 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                31                189 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                32                188 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                32                188 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                200 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                200 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                216 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                216 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                212 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                212 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                28                192 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                28                192 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                24                196 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                24                196 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                208 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                208 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                214 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                214 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                15                205 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                15                205 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                16                204 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                16                204 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                210 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                210 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                76                144 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                76                144 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                212 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                212 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                205 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                205 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               214 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               214 
[1] "data2feature, selection=ALL"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 220 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 220 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
D1V2, multiclass
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                92
  CLUS_2               4                46
  CLUS_3               0                76
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                97
  CLUS_2               3                31
  CLUS_3               0                58
  CLUS_4               0                23
D1V5, multiclass
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                32
  CLUS_2               6               111
  CLUS_3               0                69
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                47
  CLUS_2               2                48
  CLUS_3               0                32
  CLUS_4               1                86
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                87
  CLUS_2               1                12
  CLUS_3               4               114

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                92
  CLUS_2               6                44
  CLUS_3               0                76
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                95
  CLUS_2               3                31
  CLUS_3               0                58
  CLUS_4               0                23
D2V5, multiclass
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                32
  CLUS_2               6               111
  CLUS_3               2                67
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                47
  CLUS_2               1                49
  CLUS_3               1                31
  CLUS_4               3                84
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                85
  CLUS_2               1                12
  CLUS_3               4               114

Clustering(3) Variable = 6p gain mutation analysis
D3V1, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D3V2, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D3V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                92
  CLUS_2               2                48
  CLUS_3               0                76
D3V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                96
  CLUS_2               0                34
  CLUS_3               0                58
  CLUS_4               0                23
D3V5, multiclass
D3V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                32
  CLUS_2               4               113
  CLUS_3               0                69
D3V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                48
  CLUS_2               2                48
  CLUS_3               0                32
  CLUS_4               0                87
D3V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                87
  CLUS_2               0                13
  CLUS_3               3               115

Clustering(4) Variable = 7p gain mutation analysis
D4V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                10
  CLUS_3               2                 6
D4V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                 5
  CLUS_3               0                11
D4V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                89
  CLUS_2              30                20
  CLUS_3               2                74
D4V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              12                88
  CLUS_2              21                13
  CLUS_3               2                56
  CLUS_4               1                22
D4V5, multiclass
D4V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                30
  CLUS_2              31                86
  CLUS_3               4                65
D4V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              14                36
  CLUS_2              14                36
  CLUS_3               1                31
  CLUS_4               8                79
D4V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                81
  CLUS_2               2                11
  CLUS_3              28                90

Clustering(5) Variable = 7q gain mutation analysis
D5V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                10
  CLUS_3               2                 6
D5V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 5
  CLUS_3               0                11
D5V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              10                84
  CLUS_2              34                16
  CLUS_3               7                69
D5V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              20                80
  CLUS_2              23                11
  CLUS_3               6                52
  CLUS_4               1                22
D5V5, multiclass
D5V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                28
  CLUS_2              38                79
  CLUS_3               8                61
D5V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15                35
  CLUS_2              19                31
  CLUS_3               3                29
  CLUS_4              14                73
D5V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15                73
  CLUS_2               2                11
  CLUS_3              34                84

Clustering(6) Variable = 8p gain mutation analysis
D6V1, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D6V2, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D6V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10                84
  CLUS_2               3                47
  CLUS_3               1                75
D6V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              10                90
  CLUS_2               2                32
  CLUS_3               1                57
  CLUS_4               1                22
D6V5, multiclass
D6V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                31
  CLUS_2              10               107
  CLUS_3               3                66
D6V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6                44
  CLUS_2               4                46
  CLUS_3               1                31
  CLUS_4               3                84
D6V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                84
  CLUS_2               0                13
  CLUS_3              10               108

Clustering(7) Variable = 8q gain mutation analysis
D7V1, multiclass
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140        TCGA-DH-5141 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"8Q GAIN WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DH-5140        TCGA-DH-5141 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-E1-5322 
"8Q GAIN WILD-TYPE" 
D7V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              13                81
  CLUS_2               3                47
  CLUS_3               1                75
D7V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              13                87
  CLUS_2               2                32
  CLUS_3               1                57
  CLUS_4               1                22
D7V5, multiclass
D7V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                31
  CLUS_2              13               104
  CLUS_3               3                66
D7V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                43
  CLUS_2               5                45
  CLUS_3               2                30
  CLUS_4               3                84
D7V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                84
  CLUS_2               0                13
  CLUS_3              13               105

Clustering(8) Variable = 9p gain mutation analysis
D8V1, multiclass
D8V2, multiclass
D8V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                92
  CLUS_2               2                48
  CLUS_3               0                76
D8V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                97
  CLUS_2               1                33
  CLUS_3               0                58
  CLUS_4               0                23
D8V5, multiclass
D8V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                32
  CLUS_2               3               114
  CLUS_3               1                68
D8V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                49
  CLUS_2               1                49
  CLUS_3               0                32
  CLUS_4               2                85
D8V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                86
  CLUS_2               1                12
  CLUS_3               1               117

Clustering(9) Variable = 9q gain mutation analysis
D9V1, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D9V2, multiclass
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DB-5277        TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5140        TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DH-5144        TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5311 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D9V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                92
  CLUS_2               4                46
  CLUS_3               0                76
D9V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                96
  CLUS_2               2                32
  CLUS_3               0                58
  CLUS_4               0                23
D9V5, multiclass
D9V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                32
  CLUS_2               5               112
  CLUS_3               1                68
D9V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                48
  CLUS_2               2                48
  CLUS_3               0                32
  CLUS_4               2                85
D9V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                86
  CLUS_2               1                12
  CLUS_3               3               115

Clustering(10) Variable = 10p gain mutation analysis
D10V1, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5318 
"10P GAIN WILD-TYPE" 
D10V2, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-E1-5318 
"10P GAIN WILD-TYPE" 
D10V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               20                 74
  CLUS_2                0                 50
  CLUS_3                1                 75
D10V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               20                 80
  CLUS_2                0                 34
  CLUS_3                0                 58
  CLUS_4                1                 22
D10V5, multiclass
D10V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                 32
  CLUS_2               14                103
  CLUS_3                7                 62
D10V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                6                 44
  CLUS_2                6                 44
  CLUS_3                1                 31
  CLUS_4                8                 79
D10V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                9                 79
  CLUS_2                1                 12
  CLUS_3               11                107

Clustering(11) Variable = 11p gain mutation analysis
D11V1, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D11V2, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D11V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 91
  CLUS_2                1                 49
  CLUS_3                5                 71
D11V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 96
  CLUS_2                0                 34
  CLUS_3                5                 53
  CLUS_4                0                 23
D11V5, multiclass
D11V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                5                 27
  CLUS_2                4                113
  CLUS_3                0                 69
D11V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                2                 48
  CLUS_3                3                 29
  CLUS_4                1                 86
D11V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 86
  CLUS_2                0                 13
  CLUS_3                7                111

Clustering(12) Variable = 11q gain mutation analysis
D12V1, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D12V2, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D12V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                7                 87
  CLUS_2                1                 49
  CLUS_3                6                 70
D12V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                8                 92
  CLUS_2                0                 34
  CLUS_3                5                 53
  CLUS_4                1                 22
D12V5, multiclass
D12V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                5                 27
  CLUS_2                6                111
  CLUS_3                3                 66
D12V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                3                 47
  CLUS_3                3                 29
  CLUS_4                4                 83
D12V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 84
  CLUS_2                1                 12
  CLUS_3                9                109

Clustering(13) Variable = 12p gain mutation analysis
D13V1, multiclass
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5274 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5276         TCGA-DB-5277         TCGA-DB-5278 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5280         TCGA-DB-5281         TCGA-DH-5140 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"12P GAIN WILD-TYPE" 
D13V2, multiclass
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5274 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5276         TCGA-DB-5277         TCGA-DB-5278 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DB-5280         TCGA-DB-5281         TCGA-DH-5140 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"12P GAIN WILD-TYPE" 
D13V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                 85
  CLUS_2                1                 49
  CLUS_3                1                 75
D13V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                 91
  CLUS_2                0                 34
  CLUS_3                1                 57
  CLUS_4                1                 22
D13V5, multiclass
D13V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 31
  CLUS_2                9                108
  CLUS_3                1                 68
D13V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                6                 44
  CLUS_3                1                 31
  CLUS_4                1                 86
D13V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 87
  CLUS_2                0                 13
  CLUS_3               10                108

Clustering(14) Variable = 12q gain mutation analysis
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 91
  CLUS_2                1                 49
  CLUS_3                1                 75
D14V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 96
  CLUS_2                0                 34
  CLUS_3                1                 57
  CLUS_4                0                 23
D14V5, multiclass
D14V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 31
  CLUS_2                4                113
  CLUS_3                0                 69
D14V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                3                 47
  CLUS_3                0                 32
  CLUS_4                0                 87
D14V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 88
  CLUS_2                0                 13
  CLUS_3                5                113

Clustering(15) Variable = 18p gain mutation analysis
D15V1, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D15V2, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 92
  CLUS_2                2                 48
  CLUS_3                0                 76
D15V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 97
  CLUS_2                1                 33
  CLUS_3                0                 58
  CLUS_4                0                 23
D15V5, multiclass
D15V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 32
  CLUS_2                4                113
  CLUS_3                0                 69
D15V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                0                 50
  CLUS_3                1                 31
  CLUS_4                1                 86
D15V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 88
  CLUS_2                1                 12
  CLUS_3                3                115

Clustering(16) Variable = 19p gain mutation analysis
D16V1, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D16V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 92
  CLUS_2                9                 41
  CLUS_3                0                 76
D16V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 97
  CLUS_2                8                 26
  CLUS_3                0                 58
  CLUS_4                0                 23
D16V5, multiclass
D16V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 32
  CLUS_2               10                107
  CLUS_3                0                 69
D16V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                5                 45
  CLUS_3                0                 32
  CLUS_4                2                 85
D16V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 87
  CLUS_2                1                 12
  CLUS_3                9                109

Clustering(17) Variable = 19q gain mutation analysis
D17V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D17V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D17V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 92
  CLUS_2                7                 43
  CLUS_3                0                 76
D17V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 98
  CLUS_2                6                 28
  CLUS_3                0                 58
  CLUS_4                0                 23
D17V5, multiclass
D17V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 32
  CLUS_2                9                108
  CLUS_3                0                 69
D17V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                5                 45
  CLUS_3                0                 32
  CLUS_4                2                 85
D17V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 87
  CLUS_2                0                 13
  CLUS_3                8                110

Clustering(18) Variable = 20p gain mutation analysis
D18V1, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20P GAIN WILD-TYPE" 
D18V2, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20P GAIN WILD-TYPE" 
D18V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                 90
  CLUS_2               12                 38
  CLUS_3                1                 75
D18V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                6                 94
  CLUS_2               10                 24
  CLUS_3                1                 57
  CLUS_4                0                 23
D18V5, multiclass
D18V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 31
  CLUS_2               12                105
  CLUS_3                3                 66
D18V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                8                 42
  CLUS_3                0                 32
  CLUS_4                4                 83
D18V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                 84
  CLUS_2                1                 12
  CLUS_3               12                106

Clustering(19) Variable = 20q gain mutation analysis
D19V1, multiclass
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20Q GAIN WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5396 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-E1-5322 
"20Q GAIN WILD-TYPE" 
D19V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 90
  CLUS_2               11                 39
  CLUS_3                1                 75
D19V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                 95
  CLUS_2               10                 24
  CLUS_3                1                 57
  CLUS_4                0                 23
D19V5, multiclass
D19V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                1                 31
  CLUS_2               13                104
  CLUS_3                1                 68
D19V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                7                 43
  CLUS_2                7                 43
  CLUS_3                0                 32
  CLUS_4                2                 85
D19V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                 86
  CLUS_2                1                 12
  CLUS_3               13                105

Clustering(20) Variable = 21q gain mutation analysis
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 94
  CLUS_2                1                 49
  CLUS_3                2                 74
D20V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 99
  CLUS_2                0                 34
  CLUS_3                2                 56
  CLUS_4                0                 23
D20V5, multiclass
D20V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 30
  CLUS_2                1                116
  CLUS_3                0                 69
D20V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                1                 49
  CLUS_3                0                 32
  CLUS_4                1                 86
D20V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 87
  CLUS_2                0                 13
  CLUS_3                2                116

Clustering(21) Variable = 1p loss mutation analysis
D21V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               7                 3
  CLUS_3               2                 6
D21V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                 5
  CLUS_3               7                 4
D21V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                94
  CLUS_2               0                50
  CLUS_3              67                 9
D21V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0               100
  CLUS_2               0                34
  CLUS_3              58                 0
  CLUS_4               6                17
D21V5, multiclass
D21V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              32                 0
  CLUS_2               4               113
  CLUS_3              31                38
D21V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                47
  CLUS_2               0                50
  CLUS_3              25                 7
  CLUS_4              39                48
D21V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1              42                46
  CLUS_2               3                10
  CLUS_3              22                96

Clustering(22) Variable = 1q loss mutation analysis
D22V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               3                 7
  CLUS_3               0                 8
D22V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                 7
  CLUS_3               3                 8
D22V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                94
  CLUS_2               0                50
  CLUS_3               9                67
D22V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0               100
  CLUS_2               0                34
  CLUS_3               9                49
  CLUS_4               0                23
D22V5, multiclass
D22V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               5                27
  CLUS_2               0               117
  CLUS_3               4                65
D22V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               0                50
  CLUS_3               4                28
  CLUS_4               5                82
D22V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               5                83
  CLUS_2               0                13
  CLUS_3               4               114

Clustering(23) Variable = 2p loss mutation analysis
D23V1, multiclass
D23V2, multiclass
D23V3, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                93
  CLUS_2               1                49
  CLUS_3               2                74
D23V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                98
  CLUS_2               1                33
  CLUS_3               1                57
  CLUS_4               0                23
D23V5, multiclass
D23V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                31
  CLUS_2               3               114
  CLUS_3               0                69
D23V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               2                48
  CLUS_3               1                31
  CLUS_4               1                86
D23V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                88
  CLUS_2               1                12
  CLUS_3               3               115

Clustering(24) Variable = 2q loss mutation analysis
D24V1, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D24V2, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D24V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                92
  CLUS_2               0                50
  CLUS_3               1                75
D24V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                98
  CLUS_2               0                34
  CLUS_3               1                57
  CLUS_4               0                23
D24V5, multiclass
D24V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                31
  CLUS_2               2               115
  CLUS_3               0                69
D24V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               1                49
  CLUS_3               2                30
  CLUS_4               0                87
D24V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                88
  CLUS_2               0                13
  CLUS_3               3               115

Clustering(25) Variable = 3p loss mutation analysis
D25V1, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D25V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                91
  CLUS_2               0                50
  CLUS_3               1                75
D25V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                97
  CLUS_2               1                33
  CLUS_3               0                58
  CLUS_4               0                23
D25V5, multiclass
D25V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                32
  CLUS_2               4               113
  CLUS_3               0                69
D25V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                49
  CLUS_2               2                48
  CLUS_3               1                31
  CLUS_4               0                87
D25V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                88
  CLUS_2               0                13
  CLUS_3               4               114

Clustering(26) Variable = 3q loss mutation analysis
D26V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               0                10
  CLUS_3               2                 6
D26V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 6
  CLUS_3               1                10
D26V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               7                87
  CLUS_2               1                49
  CLUS_3               1                75
D26V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               8                92
  CLUS_2               1                33
  CLUS_3               0                58
  CLUS_4               0                23
D26V5, multiclass
D26V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                32
  CLUS_2               7               110
  CLUS_3               2                67
D26V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                48
  CLUS_2               3                47
  CLUS_3               1                31
  CLUS_4               3                84
D26V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                85
  CLUS_2               0                13
  CLUS_3               6               112

Clustering(27) Variable = 4p loss mutation analysis
D27V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                 8
  CLUS_3               2                 6
D27V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                 6
  CLUS_3               3                 8
D27V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                92
  CLUS_2               1                49
  CLUS_3              12                64
D27V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                97
  CLUS_2               0                34
  CLUS_3              12                46
  CLUS_4               0                23
D27V5, multiclass
D27V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7                25
  CLUS_2               2               115
  CLUS_3               6                63
D27V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               0                50
  CLUS_3               9                23
  CLUS_4               6                81
D27V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7                81
  CLUS_2               0                13
  CLUS_3               8               110

Clustering(28) Variable = 4q loss mutation analysis
D28V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                 8
  CLUS_3               2                 6
D28V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 6
  CLUS_3               3                 8
D28V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                86
  CLUS_2               1                49
  CLUS_3              15                61
D28V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                92
  CLUS_2               0                34
  CLUS_3              15                43
  CLUS_4               1                22
D28V5, multiclass
D28V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9                23
  CLUS_2               7               110
  CLUS_3               7                62
D28V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                49
  CLUS_2               2                48
  CLUS_3              11                21
  CLUS_4              10                77
D28V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11                77
  CLUS_2               2                11
  CLUS_3              11               107

Clustering(29) Variable = 5p loss mutation analysis
D29V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               2                 8
  CLUS_3               1                 7
D29V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                 7
  CLUS_2               0                 7
  CLUS_3               3                 8
D29V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               8                86
  CLUS_2               3                47
  CLUS_3               0                76
D29V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1              10                90
  CLUS_2               1                33
  CLUS_3               0                58
  CLUS_4               0                23
D29V5, multiclass
D29V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                32
  CLUS_2               8               109
  CLUS_3               3                66
D29V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               3                47
  CLUS_3               3                29
  CLUS_4               5                82
D29V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               4                84
  CLUS_2               1                12
  CLUS_3               6               112

Clustering(30) Variable = 5q loss mutation analysis
D30V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               2                 8
  CLUS_3               1                 7
D30V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               0                 7
  CLUS_3               3                 8
D30V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6                88
  CLUS_2               3                47
  CLUS_3               0                76
D30V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8                92
  CLUS_2               1                33
  CLUS_3               0                58
  CLUS_4               0                23
D30V5, multiclass
D30V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                32
  CLUS_2               9               108
  CLUS_3               0                69
D30V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               6                44
  CLUS_3               2                30
  CLUS_4               1                86
D30V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                87
  CLUS_2               1                12
  CLUS_3               7               111

Clustering(31) Variable = 6p loss mutation analysis
D31V1, multiclass
D31V2, multiclass
D31V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                92
  CLUS_2               4                46
  CLUS_3               1                75
D31V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                99
  CLUS_2               4                30
  CLUS_3               1                57
  CLUS_4               1                22
D31V5, multiclass
D31V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                31
  CLUS_2               4               113
  CLUS_3               2                67
D31V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                47
  CLUS_2               1                49
  CLUS_3               1                31
  CLUS_4               2                85
D31V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                87
  CLUS_2               1                12
  CLUS_3               5               113

Clustering(32) Variable = 6q loss mutation analysis
D32V1, multiclass
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-5390        TCGA-CS-5394 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5281        TCGA-DH-5140        TCGA-DH-5141 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"6Q LOSS WILD-TYPE" 
D32V2, multiclass
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-5390        TCGA-CS-5394 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5281        TCGA-DH-5140        TCGA-DH-5141 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-E1-5322 
"6Q LOSS WILD-TYPE" 
D32V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                87
  CLUS_2              11                39
  CLUS_3               3                73
D32V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12                88
  CLUS_2               7                27
  CLUS_3               1                57
  CLUS_4               1                22
D32V5, multiclass
D32V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                31
  CLUS_2              14               103
  CLUS_3               6                63
D32V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              10                40
  CLUS_2               3                47
  CLUS_3               1                31
  CLUS_4               7                80
D32V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                82
  CLUS_2               2                11
  CLUS_3              13               105

Clustering(33) Variable = 8p loss mutation analysis
D33V1, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5141 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5322 
"8P LOSS WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-CS-5396        TCGA-DB-5270 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5273        TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5141 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144        TCGA-E1-5302 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-E1-5322 
"8P LOSS WILD-TYPE" 
D33V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                93
  CLUS_2               2                48
  CLUS_3               0                76
D33V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                99
  CLUS_2               2                32
  CLUS_3               0                58
  CLUS_4               0                23
D33V5, multiclass
D33V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                32
  CLUS_2               2               115
  CLUS_3               1                68
D33V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               0                50
  CLUS_3               2                30
  CLUS_4               1                86
D33V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                88
  CLUS_2               0                13
  CLUS_3               3               115

Clustering(34) Variable = 9p loss mutation analysis
D34V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 9
  CLUS_3               3                 5
D34V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               2                 5
  CLUS_3               2                 9
D34V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              13                81
  CLUS_2              17                33
  CLUS_3               8                68
D34V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              22                78
  CLUS_2               8                26
  CLUS_3               6                52
  CLUS_4               1                22
D34V5, multiclass
D34V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                27
  CLUS_2              25                92
  CLUS_3               8                61
D34V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9                41
  CLUS_2               9                41
  CLUS_3               7                25
  CLUS_4              13                74
D34V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              14                74
  CLUS_2               2                11
  CLUS_3              22                96

Clustering(35) Variable = 9q loss mutation analysis
D35V1, multiclass
D35V2, multiclass
D35V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                93
  CLUS_2               0                50
  CLUS_3               5                71
D35V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                99
  CLUS_2               0                34
  CLUS_3               5                53
  CLUS_4               0                23
D35V5, multiclass
D35V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                28
  CLUS_2               0               117
  CLUS_3               2                67
D35V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                50
  CLUS_2               0                50
  CLUS_3               4                28
  CLUS_4               2                85
D35V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                85
  CLUS_2               0                13
  CLUS_3               3               115

Clustering(36) Variable = 10p loss mutation analysis
D36V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                  9
  CLUS_3                2                  6
D36V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                  5
  CLUS_3                1                 10
D36V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 93
  CLUS_2               27                 23
  CLUS_3                3                 73
D36V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 99
  CLUS_2               26                  8
  CLUS_3                3                 55
  CLUS_4                0                 23
D36V5, multiclass
D36V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 31
  CLUS_2               25                 92
  CLUS_3                4                 65
D36V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               12                 38
  CLUS_2               10                 40
  CLUS_3                3                 29
  CLUS_4                6                 81
D36V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                5                 83
  CLUS_2                2                 11
  CLUS_3               24                 94

Clustering(37) Variable = 10q loss mutation analysis
D37V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                1                  9
  CLUS_3                2                  6
D37V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                2                  5
  CLUS_3                1                 10
D37V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 92
  CLUS_2               27                 23
  CLUS_3                3                 73
D37V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 98
  CLUS_2               26                  8
  CLUS_3                3                 55
  CLUS_4                0                 23
D37V5, multiclass
D37V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 31
  CLUS_2               26                 91
  CLUS_3                4                 65
D37V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                 38
  CLUS_2               11                 39
  CLUS_3                3                 29
  CLUS_4                6                 81
D37V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 82
  CLUS_2                2                 11
  CLUS_3               24                 94

Clustering(38) Variable = 11p loss mutation analysis
D38V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                1                  9
  CLUS_3                1                  7
D38V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                0                  7
  CLUS_3                2                  9
D38V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               15                 79
  CLUS_2                4                 46
  CLUS_3                1                 75
D38V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               17                 83
  CLUS_2                2                 32
  CLUS_3                0                 58
  CLUS_4                1                 22
D38V5, multiclass
D38V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 32
  CLUS_2               17                100
  CLUS_3                3                 66
D38V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2               11                 39
  CLUS_3                1                 31
  CLUS_4                5                 82
D38V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                4                 84
  CLUS_2                3                 10
  CLUS_3               13                105

Clustering(39) Variable = 11q loss mutation analysis
D39V1, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D39V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 94
  CLUS_2                4                 46
  CLUS_3                0                 76
D39V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 98
  CLUS_2                2                 32
  CLUS_3                0                 58
  CLUS_4                0                 23
D39V5, multiclass
D39V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 32
  CLUS_2                4                113
  CLUS_3                0                 69
D39V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                2                 48
  CLUS_3                0                 32
  CLUS_4                1                 86
D39V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 88
  CLUS_2                1                 12
  CLUS_3                3                115

Clustering(40) Variable = 12q loss mutation analysis
D40V1, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D40V2, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D40V3, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                7                 87
  CLUS_2                0                 50
  CLUS_3                1                 75
D40V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                7                 93
  CLUS_2                0                 34
  CLUS_3                1                 57
  CLUS_4                0                 23
D40V5, multiclass
D40V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 32
  CLUS_2                6                111
  CLUS_3                2                 67
D40V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 50
  CLUS_2                4                 46
  CLUS_3                1                 31
  CLUS_4                3                 84
D40V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 84
  CLUS_2                0                 13
  CLUS_3                4                114

Clustering(41) Variable = 13q loss mutation analysis
D41V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                2                  8
  CLUS_3                1                  7
D41V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  7
  CLUS_2                0                  7
  CLUS_3                3                  8
D41V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               10                 84
  CLUS_2                8                 42
  CLUS_3               10                 66
D41V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               15                 85
  CLUS_2                6                 28
  CLUS_3                7                 51
  CLUS_4                0                 23
D41V5, multiclass
D41V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 28
  CLUS_2               17                100
  CLUS_3                6                 63
D41V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                7                 43
  CLUS_2                6                 44
  CLUS_3                5                 27
  CLUS_4               10                 77
D41V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                8                 80
  CLUS_2                2                 11
  CLUS_3               18                100

Clustering(42) Variable = 14q loss mutation analysis
D42V1, multiclass
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5395         TCGA-CS-5396 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"14Q LOSS WILD-TYPE" 
D42V2, multiclass
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4943         TCGA-CS-4944         TCGA-CS-5390 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CS-5394         TCGA-CS-5395         TCGA-CS-5396 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5270         TCGA-DB-5273         TCGA-DB-5274 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5275         TCGA-DB-5276         TCGA-DB-5277 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DB-5278         TCGA-DB-5280         TCGA-DB-5281 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5141         TCGA-DH-5142         TCGA-DH-5143 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DH-5144         TCGA-E1-5302         TCGA-E1-5303 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5304         TCGA-E1-5311         TCGA-E1-5318 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"14Q LOSS WILD-TYPE" 
D42V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 89
  CLUS_2               13                 37
  CLUS_3                6                 70
D42V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 92
  CLUS_2               11                 23
  CLUS_3                5                 53
  CLUS_4                0                 23
D42V5, multiclass
D42V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                 30
  CLUS_2               16                101
  CLUS_3                6                 63
D42V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               12                 38
  CLUS_2                2                 48
  CLUS_3                3                 29
  CLUS_4                7                 80
D42V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 83
  CLUS_2                2                 11
  CLUS_3               17                101

Clustering(43) Variable = 15q loss mutation analysis
D43V1, multiclass
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D43V2, multiclass
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DH-5142         TCGA-DH-5143         TCGA-DH-5144 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5302         TCGA-E1-5303         TCGA-E1-5304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D43V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 93
  CLUS_2                2                 48
  CLUS_3                9                 67
D43V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 98
  CLUS_2                1                 33
  CLUS_3                9                 49
  CLUS_4                0                 23
D43V5, multiclass
D43V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 26
  CLUS_2                3                114
  CLUS_3                3                 66
D43V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                1                 49
  CLUS_3                4                 28
  CLUS_4                4                 83
D43V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 82
  CLUS_2                0                 13
  CLUS_3                6                112

Clustering(44) Variable = 16q loss mutation analysis
D44V1, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D44V2, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 26 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5140         TCGA-DH-5141         TCGA-DH-5142 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5304         TCGA-E1-5311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-E1-5318         TCGA-E1-5322 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D44V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 91
  CLUS_2                2                 48
  CLUS_3                1                 75
D44V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 97
  CLUS_2                3                 31
  CLUS_3                0                 58
  CLUS_4                0                 23
D44V5, multiclass
D44V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 32
  CLUS_2                5                112
  CLUS_3                1                 68
D44V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                1                 49
  CLUS_3                0                 32
  CLUS_4                2                 85
D44V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 86
  CLUS_2                0                 13
  CLUS_3                4                114

Clustering(45) Variable = 18p loss mutation analysis
D45V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                3                  7
  CLUS_3                0                  8
D45V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                0                  7
  CLUS_3                3                  8
D45V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 91
  CLUS_2                4                 46
  CLUS_3                8                 68
D45V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 96
  CLUS_2                3                 31
  CLUS_3                8                 50
  CLUS_4                0                 23
D45V5, multiclass
D45V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 27
  CLUS_2                6                111
  CLUS_3                4                 65
D45V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                2                 48
  CLUS_3                6                 26
  CLUS_4                5                 82
D45V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 84
  CLUS_2                0                 13
  CLUS_3               11                107

Clustering(46) Variable = 18q loss mutation analysis
D46V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                3                  7
  CLUS_3                0                  8
D46V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  9
  CLUS_2                0                  7
  CLUS_3                3                  8
D46V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 93
  CLUS_2                5                 45
  CLUS_3               10                 66
D46V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 97
  CLUS_2                3                 31
  CLUS_3               10                 48
  CLUS_4                0                 23
D46V5, multiclass
D46V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                6                 26
  CLUS_2                5                112
  CLUS_3                5                 64
D46V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                1                 49
  CLUS_3                7                 25
  CLUS_4                6                 81
D46V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 83
  CLUS_2                0                 13
  CLUS_3               11                107

Clustering(47) Variable = 19p loss mutation analysis
D47V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                4                  6
  CLUS_3                1                  7
D47V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                0                  7
  CLUS_3                5                  6
D47V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 93
  CLUS_2                3                 47
  CLUS_3                6                 70
D47V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 97
  CLUS_2                1                 33
  CLUS_3                6                 52
  CLUS_4                0                 23
D47V5, multiclass
D47V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 28
  CLUS_2                2                115
  CLUS_3                4                 65
D47V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                0                 50
  CLUS_3                5                 27
  CLUS_4                4                 83
D47V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 85
  CLUS_2                0                 13
  CLUS_3                7                111

Clustering(48) Variable = 19q loss mutation analysis
D48V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                7                  3
  CLUS_3                3                  5
D48V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                  6
  CLUS_2                2                  5
  CLUS_3                8                  3
D48V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 92
  CLUS_2                3                 47
  CLUS_3               71                  5
D48V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                8                 92
  CLUS_2                2                 32
  CLUS_3               57                  1
  CLUS_4                6                 17
D48V5, multiclass
D48V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               32                  0
  CLUS_2                9                108
  CLUS_3               35                 34
D48V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                3                 47
  CLUS_3               26                  6
  CLUS_4               43                 44
D48V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               46                 42
  CLUS_2                2                 11
  CLUS_3               28                 90

Clustering(49) Variable = 21q loss mutation analysis
D49V1, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"21Q LOSS WILD-TYPE" 
D49V2, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 25 
        TCGA-CS-4942         TCGA-CS-4943         TCGA-CS-4944 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5390         TCGA-CS-5394         TCGA-CS-5395 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CS-5396         TCGA-DB-5270         TCGA-DB-5273 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5274         TCGA-DB-5275         TCGA-DB-5276 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5277         TCGA-DB-5278         TCGA-DB-5280 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DB-5281         TCGA-DH-5140         TCGA-DH-5141 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DH-5143         TCGA-DH-5144         TCGA-E1-5302 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5303         TCGA-E1-5311         TCGA-E1-5318 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-E1-5322 
"21Q LOSS WILD-TYPE" 
D49V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 91
  CLUS_2                3                 47
  CLUS_3                2                 74
D49V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 95
  CLUS_2                2                 32
  CLUS_3                1                 57
  CLUS_4                0                 23
D49V5, multiclass
D49V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 32
  CLUS_2                6                111
  CLUS_3                2                 67
D49V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                4                 46
  CLUS_3                0                 32
  CLUS_4                3                 84
D49V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 87
  CLUS_2                1                 12
  CLUS_3                6                112

Clustering(50) Variable = 22q loss mutation analysis
D50V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                1                  9
  CLUS_3                1                  7
D50V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                0                  7
  CLUS_3                2                  9
D50V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 90
  CLUS_2               11                 39
  CLUS_3                0                 76
D50V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 94
  CLUS_2                9                 25
  CLUS_3                0                 58
  CLUS_4                0                 23
D50V5, multiclass
D50V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 32
  CLUS_2               12                105
  CLUS_3                2                 67
D50V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 44
  CLUS_2                5                 45
  CLUS_3                1                 31
  CLUS_4                3                 84
D50V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 85
  CLUS_2                0                 13
  CLUS_3               12                106

Clustering(51) Variable = Xq loss mutation analysis
D51V1, multiclass
D51V2, multiclass
D51V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                90
  CLUS_2               2                48
  CLUS_3               0                76
D51V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               5                95
  CLUS_2               1                33
  CLUS_3               0                58
  CLUS_4               0                23
D51V5, multiclass
D51V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                32
  CLUS_2               6               111
  CLUS_3               0                69
D51V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                47
  CLUS_2               2                48
  CLUS_3               0                32
  CLUS_4               1                86
D51V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                87
  CLUS_2               1                12
  CLUS_3               4               114
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
