
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_cnvs_onlysig.2.4054/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/376238/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/READ-TP/2909295/1.GDAC_mergedClustering.Finished/READ-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=READ-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=READ-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=166, in cluster file=162, common to both=162
[1]  62 162
[1] "Amp Peak  1(1q21.3) mutation analysis"
[1] 3
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           48                           114 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           48                           114 
[1] "Amp Peak  2(1q32.2) mutation analysis"
[1] 3
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           48                           114 
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           48                           114 
[1] "Amp Peak  3(5q22.3) mutation analysis"
[1] 3
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           19                           143 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           19                           143 
[1] "Amp Peak  4(6p21.1) mutation analysis"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           52                           110 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           52                           110 
[1] "Amp Peak  5(8p11.23) mutation analysis"
[1] 3
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            52                            110 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            52                            110 
[1] "Amp Peak  6(8p11.21) mutation analysis"
[1] 3
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            69                             93 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            69                             93 
[1] "Amp Peak  7(8q24.21) mutation analysis"
[1] 3
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           107                             55 
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           107                             55 
[1] "Amp Peak  8(10q22.2) mutation analysis"
[1] 3
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            151 
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            151 
[1] "Amp Peak  9(11p15.5) mutation analysis"
[1] 3
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            43                            119 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            43                            119 
[1] "Amp Peak 10(11q13.3) mutation analysis"
[1] 3
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            26                            136 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            26                            136 
[1] "Amp Peak 11(12p13.33) mutation analysis"
[1] 3
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             41                             121 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             41                             121 
[1] "Amp Peak 12(12p12.1) mutation analysis"
[1] 3
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            40                            122 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            40                            122 
[1] "Amp Peak 13(13q12.13) mutation analysis"
[1] 3
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            121                              41 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            121                              41 
[1] "Amp Peak 14(13q12.2) mutation analysis"
[1] 3
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           120                             42 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           120                             42 
[1] "Amp Peak 15(13q22.1) mutation analysis"
[1] 3
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           117                             45 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           117                             45 
[1] "Amp Peak 16(15q26.1) mutation analysis"
[1] 3
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            15                            147 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            15                            147 
[1] "Amp Peak 17(16p11.2) mutation analysis"
[1] 3
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            45                            117 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            45                            117 
[1] "Amp Peak 18(17q12) mutation analysis"
[1] 3
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          43                          119 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          43                          119 
[1] "Amp Peak 19(17q24.1) mutation analysis"
[1] 3
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            37                            125 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            37                            125 
[1] "Amp Peak 20(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            32                            130 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            32                            130 
[1] "Amp Peak 21(20q11.21) mutation analysis"
[1] 3
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            143                              19 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            143                              19 
[1] "Amp Peak 22(20q11.23) mutation analysis"
[1] 3
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            144                              18 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            144                              18 
[1] "Amp Peak 23(20q13.31) mutation analysis"
[1] 3
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                            145                              17 
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                            145                              17 
[1] "Amp Peak 24(Xp22.2) mutation analysis"
[1] 3
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           33                           129 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           33                           129 
[1] "Amp Peak 25(Xq27.3) mutation analysis"
[1] 3
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                           38                           124 
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                           38                           124 
[1] "Del Peak  1(1p36.11) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            71                             91 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            71                             91 
[1] "Del Peak  2(1p33) mutation analysis"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         49                         113 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         49                         113 
[1] "Del Peak  3(1p13.2) mutation analysis"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           51                           111 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           51                           111 
[1] "Del Peak  4(2p12) mutation analysis"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         17                         145 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         17                         145 
[1] "Del Peak  5(3p14.2) mutation analysis"
[1] 3
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           29                           133 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           29                           133 
[1] "Del Peak  6(3q26.31) mutation analysis"
[1] 3
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            17                            145 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            17                            145 
[1] "Del Peak  7(4p13) mutation analysis"
[1] 3
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         58                         104 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         58                         104 
[1] "Del Peak  8(4q22.1) mutation analysis"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           72                            90 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           72                            90 
[1] "Del Peak  9(4q35.1) mutation analysis"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           72                            90 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           72                            90 
[1] "Del Peak 10(5q11.2) mutation analysis"
[1] 3
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                           49                           113 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                           49                           113 
[1] "Del Peak 11(5q22.2) mutation analysis"
[1] 3
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           55                           107 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           55                           107 
[1] "Del Peak 12(6p25.3) mutation analysis"
[1] 3
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           24                           138 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           24                           138 
[1] "Del Peak 13(6q26) mutation analysis"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         30                         132 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         30                         132 
[1] "Del Peak 14(7q31.1) mutation analysis"
[1] 3
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           158 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           158 
[1] "Del Peak 15(8p23.2) mutation analysis"
[1] 3
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          100                            62 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          100                            62 
[1] "Del Peak 16(8p11.21) mutation analysis"
[1] 3
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            24                            138 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            24                            138 
[1] "Del Peak 17(10q21.1) mutation analysis"
[1] 3
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            37                            125 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            37                            125 
[1] "Del Peak 18(10q25.2) mutation analysis"
[1] 3
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            47                            115 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            47                            115 
[1] "Del Peak 19(11q22.3) mutation analysis"
[1] 3
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            37                            125 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            37                            125 
[1] "Del Peak 20(12p13.1) mutation analysis"
[1] 3
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            33                            129 
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            33                            129 
[1] "Del Peak 21(12q21.33) mutation analysis"
[1] 3
  DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE 
                             28                             134 
  DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE 
                             28                             134 
[1] "Del Peak 22(14q11.2) mutation analysis"
[1] 3
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            67                             95 
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            67                             95 
[1] "Del Peak 23(14q31.1) mutation analysis"
[1] 3
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            69                             93 
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            69                             93 
[1] "Del Peak 24(15q22.33) mutation analysis"
[1] 3
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             75                              87 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             75                              87 
[1] "Del Peak 25(16p13.3) mutation analysis"
[1] 3
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            13                            149 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            13                            149 
[1] "Del Peak 26(16q23.1) mutation analysis"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            139 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            139 
[1] "Del Peak 27(17p12) mutation analysis"
[1] 3
  DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE 
                         110                           52 
  DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE 
                         110                           52 
[1] "Del Peak 28(17p11.2) mutation analysis"
[1] 3
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           102                             60 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           102                             60 
[1] "Del Peak 29(17q25.3) mutation analysis"
[1] 3
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                            24                            138 
  DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE 
                            24                            138 
[1] "Del Peak 30(18q21.2) mutation analysis"
[1] 3
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                           143                             19 
  DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE 
                           143                             19 
[1] "Del Peak 31(18q22.1) mutation analysis"
[1] 3
  DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE 
                           138                             24 
  DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE 
                           138                             24 
[1] "Del Peak 32(19p13.3) mutation analysis"
[1] 3
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            38                            124 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            38                            124 
[1] "Del Peak 33(20p12.1) mutation analysis"
[1] 3
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            60                            102 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            60                            102 
[1] "Del Peak 34(20p12.1) mutation analysis"
[1] 3
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                            60                            102 
  DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE 
                            60                            102 
[1] "Del Peak 35(21q11.2) mutation analysis"
[1] 3
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                            70                             92 
  DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE 
                            70                             92 
[1] "Del Peak 36(22q13.31) mutation analysis"
[1] 3
  DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE 
                             66                              96 
  DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE 
                             66                              96 
[1] "Del Peak 37(Xp22.33) mutation analysis"
[1] 3
  DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE 
                            33                            129 
  DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE 
                            33                            129 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 

Input Data has 10 rows and 162 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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 162 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=7, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1q21.3) mutation analysis
D1V1, multiclass
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  CLUS_1                           6                            19
  CLUS_2                           5                            15
  CLUS_3                           6                            18
D1V2, multiclass
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  CLUS_1                           5                            14
  CLUS_2                           5                            19
  CLUS_3                           7                            19
D1V3, multiclass
D1V4, multiclass
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  CLUS_1                           9                            17
  CLUS_2                          14                            24
  CLUS_3                           9                            20
D1V5, multiclass
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  CLUS_1                           8                            25
  CLUS_2                          11                            29
  CLUS_3                          19                            34
D1V6, multiclass
D1V7, multiclass
D1V8, multiclass
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                           6                             6
  CLUS_3                           2                            17
D1V9, multiclass
D1V10, multiclass
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                          16                            47
  CLUS_3                          19                            40

Clustering(2) Variable = Amp Peak  2(1q32.2) mutation analysis
D2V1, multiclass
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  CLUS_1                           5                            20
  CLUS_2                           6                            14
  CLUS_3                           6                            18
D2V2, multiclass
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  CLUS_1                           5                            14
  CLUS_2                           6                            18
  CLUS_3                           6                            20
D2V3, multiclass
D2V4, multiclass
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  CLUS_1                           7                            19
  CLUS_2                          15                            23
  CLUS_3                          10                            19
D2V5, multiclass
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  CLUS_1                           7                            26
  CLUS_2                          11                            29
  CLUS_3                          21                            32
D2V6, multiclass
D2V7, multiclass
D2V8, multiclass
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                           5                             7
  CLUS_3                           3                            16
D2V9, multiclass
D2V10, multiclass
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                          15                            48
  CLUS_3                          20                            39

Clustering(3) Variable = Amp Peak  3(5q22.3) mutation analysis
D3V1, multiclass
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  CLUS_1                           2                            23
  CLUS_2                           0                            20
  CLUS_3                           6                            18
D3V2, multiclass
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                           2                            22
  CLUS_3                           2                            24
D3V3, multiclass
D3V4, multiclass
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  CLUS_1                           2                            24
  CLUS_2                           3                            35
  CLUS_3                           6                            23
D3V5, multiclass
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  CLUS_1                           5                            28
  CLUS_2                           7                            33
  CLUS_3                           3                            50
D3V6, multiclass
D3V7, multiclass
D3V8, multiclass
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  CLUS_1                           2                            17
  CLUS_2                           0                            12
  CLUS_3                           4                            15
D3V9, multiclass
D3V10, multiclass
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  CLUS_1                           1                            18
  CLUS_2                           6                            57
  CLUS_3                           8                            51

Clustering(4) Variable = Amp Peak  4(6p21.1) mutation analysis
D4V1, multiclass
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  CLUS_1                           3                            22
  CLUS_2                           8                            12
  CLUS_3                          10                            14
D4V2, multiclass
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  CLUS_1                           9                            10
  CLUS_2                           3                            21
  CLUS_3                           9                            17
D4V3, multiclass
D4V4, multiclass
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  CLUS_1                          14                            12
  CLUS_2                           9                            29
  CLUS_3                           8                            21
D4V5, multiclass
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  CLUS_1                          10                            23
  CLUS_2                          12                            28
  CLUS_3                          18                            35
D4V6, multiclass
D4V7, multiclass
D4V8, multiclass
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  CLUS_1                           7                            12
  CLUS_2                           5                             7
  CLUS_3                           5                            14
D4V9, multiclass
D4V10, multiclass
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  CLUS_1                           8                            11
  CLUS_2                          19                            44
  CLUS_3                          24                            35

Clustering(5) Variable = Amp Peak  5(8p11.23) mutation analysis
D5V1, multiclass
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  CLUS_1                            2                             23
  CLUS_2                            3                             17
  CLUS_3                           12                             12
D5V2, multiclass
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            4                             20
  CLUS_3                            4                             22
D5V3, multiclass
D5V4, multiclass
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  CLUS_1                           13                             13
  CLUS_2                           12                             26
  CLUS_3                           10                             19
D5V5, multiclass
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  CLUS_1                           11                             22
  CLUS_2                           17                             23
  CLUS_3                           15                             38
D5V6, multiclass
D5V7, multiclass
D5V8, multiclass
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  CLUS_1                            7                             12
  CLUS_2                            6                              6
  CLUS_3                            8                             11
D5V9, multiclass
D5V10, multiclass
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                           12                             51
  CLUS_3                           26                             33

Clustering(6) Variable = Amp Peak  6(8p11.21) mutation analysis
D6V1, multiclass
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  CLUS_1                            6                             19
  CLUS_2                            5                             15
  CLUS_3                           15                              9
D6V2, multiclass
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  CLUS_1                           12                              7
  CLUS_2                            8                             16
  CLUS_3                            6                             20
D6V3, multiclass
D6V4, multiclass
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  CLUS_1                           16                             10
  CLUS_2                           16                             22
  CLUS_3                           12                             17
D6V5, multiclass
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  CLUS_1                           12                             21
  CLUS_2                           21                             19
  CLUS_3                           25                             28
D6V6, multiclass
D6V7, multiclass
D6V8, multiclass
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            7                              5
  CLUS_3                           10                              9
D6V9, multiclass
D6V10, multiclass
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                           20                             43
  CLUS_3                           30                             29

Clustering(7) Variable = Amp Peak  7(8q24.21) mutation analysis
D7V1, multiclass
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  CLUS_1                           12                             13
  CLUS_2                           12                              8
  CLUS_3                           20                              4
D7V2, multiclass
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  CLUS_1                           17                              2
  CLUS_2                           13                             11
  CLUS_3                           14                             12
D7V3, multiclass
D7V4, multiclass
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  CLUS_1                           21                              5
  CLUS_2                           23                             15
  CLUS_3                           19                             10
D7V5, multiclass
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  CLUS_1                           22                             11
  CLUS_2                           30                             10
  CLUS_3                           35                             18
D7V6, multiclass
D7V7, multiclass
D7V8, multiclass
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  CLUS_1                           12                              7
  CLUS_2                            8                              4
  CLUS_3                           15                              4
D7V9, multiclass
D7V10, multiclass
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  CLUS_1                           16                              3
  CLUS_2                           38                             25
  CLUS_3                           40                             19

Clustering(8) Variable = Amp Peak  8(10q22.2) mutation analysis
D8V1, multiclass
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  CLUS_1                            1                             24
  CLUS_2                            3                             17
  CLUS_3                            2                             22
D8V2, multiclass
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            2                             22
  CLUS_3                            3                             23
D8V3, multiclass
D8V4, multiclass
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  CLUS_1                            1                             25
  CLUS_2                            2                             36
  CLUS_3                            2                             27
D8V5, multiclass
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  CLUS_1                            2                             31
  CLUS_2                            3                             37
  CLUS_3                            4                             49
D8V6, multiclass
D8V7, multiclass
D8V8, multiclass
D8V9, multiclass
D8V10, multiclass
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            7                             56
  CLUS_3                            2                             57

Clustering(9) Variable = Amp Peak  9(11p15.5) mutation analysis
D9V1, multiclass
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  CLUS_1                            8                             17
  CLUS_2                            3                             17
  CLUS_3                            6                             18
D9V2, multiclass
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            8                             16
  CLUS_3                            5                             21
D9V3, multiclass
D9V4, multiclass
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  CLUS_1                            8                             18
  CLUS_2                           11                             27
  CLUS_3                            6                             23
D9V5, multiclass
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  CLUS_1                            8                             25
  CLUS_2                           10                             30
  CLUS_3                           17                             36
D9V6, multiclass
D9V7, multiclass
D9V8, multiclass
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            2                             10
  CLUS_3                           11                              8
D9V9, multiclass
D9V10, multiclass
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                           16                             47
  CLUS_3                           20                             39

Clustering(10) Variable = Amp Peak 10(11q13.3) mutation analysis
D10V1, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                            0                             25
  CLUS_2                            2                             18
  CLUS_3                            5                             19
D10V2, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            0                             24
  CLUS_3                            3                             23
D10V3, multiclass
D10V4, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                           11                             15
  CLUS_2                            4                             34
  CLUS_3                            4                             25
D10V5, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                            6                             27
  CLUS_2                            6                             34
  CLUS_3                            8                             45
D10V6, multiclass
D10V7, multiclass
D10V8, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            2                             10
  CLUS_3                            6                             13
D10V9, multiclass
D10V10, multiclass
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            6                             57
  CLUS_3                           13                             46

Clustering(11) Variable = Amp Peak 11(12p13.33) mutation analysis
D11V1, multiclass
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                             5                              20
  CLUS_2                             7                              13
  CLUS_3                             5                              19
D11V2, multiclass
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                             3                              16
  CLUS_2                             6                              18
  CLUS_3                             8                              18
D11V3, multiclass
D11V4, multiclass
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                             8                              18
  CLUS_2                             8                              30
  CLUS_3                             7                              22
D11V5, multiclass
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                            12                              21
  CLUS_2                             6                              34
  CLUS_3                            13                              40
D11V6, multiclass
D11V7, multiclass
D11V8, multiclass
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                             3                              16
  CLUS_2                             5                               7
  CLUS_3                             7                              12
D11V9, multiclass
D11V10, multiclass
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  CLUS_1                             6                              13
  CLUS_2                            16                              47
  CLUS_3                            16                              43

Clustering(12) Variable = Amp Peak 12(12p12.1) mutation analysis
D12V1, multiclass
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                            5                             20
  CLUS_2                            7                             13
  CLUS_3                            6                             18
D12V2, multiclass
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            6                             18
  CLUS_3                            8                             18
D12V3, multiclass
D12V4, multiclass
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                            5                             21
  CLUS_2                            7                             31
  CLUS_3                            9                             20
D12V5, multiclass
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                           12                             21
  CLUS_2                            5                             35
  CLUS_3                           11                             42
D12V6, multiclass
D12V7, multiclass
D12V8, multiclass
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            4                              8
  CLUS_3                            6                             13
D12V9, multiclass
D12V10, multiclass
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                            7                             12
  CLUS_2                           17                             46
  CLUS_3                           13                             46

Clustering(13) Variable = Amp Peak 13(13q12.13) mutation analysis
D13V1, multiclass
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  CLUS_1                            18                               7
  CLUS_2                            12                               8
  CLUS_3                            18                               6
D13V2, multiclass
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  CLUS_1                            14                               5
  CLUS_2                            18                               6
  CLUS_3                            16                              10
D13V3, multiclass
D13V4, multiclass
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  CLUS_1                            23                               3
  CLUS_2                            29                               9
  CLUS_3                            21                               8
D13V5, multiclass
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  CLUS_1                            24                               9
  CLUS_2                            27                              13
  CLUS_3                            42                              11
D13V6, multiclass
D13V7, multiclass
D13V8, multiclass
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  CLUS_1                            14                               5
  CLUS_2                            10                               2
  CLUS_3                            18                               1
D13V9, multiclass
D13V10, multiclass
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  CLUS_1                            16                               3
  CLUS_2                            40                              23
  CLUS_3                            51                               8

Clustering(14) Variable = Amp Peak 14(13q12.2) mutation analysis
D14V1, multiclass
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  CLUS_1                           19                              6
  CLUS_2                           12                              8
  CLUS_3                           18                              6
D14V2, multiclass
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           19                              5
  CLUS_3                           16                             10
D14V3, multiclass
D14V4, multiclass
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  CLUS_1                           23                              3
  CLUS_2                           29                              9
  CLUS_3                           20                              9
D14V5, multiclass
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  CLUS_1                           24                              9
  CLUS_2                           28                             12
  CLUS_3                           41                             12
D14V6, multiclass
D14V7, multiclass
D14V8, multiclass
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           10                              2
  CLUS_3                           17                              2
D14V9, multiclass
D14V10, multiclass
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           41                             22
  CLUS_3                           51                              8

Clustering(15) Variable = Amp Peak 15(13q22.1) mutation analysis
D15V1, multiclass
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CLUS_1                           17                              8
  CLUS_2                           11                              9
  CLUS_3                           18                              6
D15V2, multiclass
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           18                              6
  CLUS_3                           14                             12
D15V3, multiclass
D15V4, multiclass
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CLUS_1                           24                              2
  CLUS_2                           29                              9
  CLUS_3                           19                             10
D15V5, multiclass
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CLUS_1                           23                             10
  CLUS_2                           28                             12
  CLUS_3                           39                             14
D15V6, multiclass
D15V7, multiclass
D15V8, multiclass
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           11                              1
  CLUS_3                           17                              2
D15V9, multiclass
D15V10, multiclass
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           39                             24
  CLUS_3                           52                              7

Clustering(16) Variable = Amp Peak 16(15q26.1) mutation analysis
D16V1, multiclass
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  CLUS_1                            0                             25
  CLUS_2                            3                             17
  CLUS_3                            2                             22
D16V2, multiclass
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            0                             24
  CLUS_3                            4                             22
D16V3, multiclass
D16V4, multiclass
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  CLUS_1                            1                             25
  CLUS_2                            5                             33
  CLUS_3                            4                             25
D16V5, multiclass
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  CLUS_1                            5                             28
  CLUS_2                            6                             34
  CLUS_3                            2                             51
D16V6, multiclass
D16V7, multiclass
D16V8, multiclass
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            0                             12
  CLUS_3                            2                             17
D16V9, multiclass
D16V10, multiclass
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            5                             58
  CLUS_3                            5                             54

Clustering(17) Variable = Amp Peak 17(16p11.2) mutation analysis
D17V1, multiclass
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  CLUS_1                            7                             18
  CLUS_2                            3                             17
  CLUS_3                           10                             14
D17V2, multiclass
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            7                             17
  CLUS_3                            4                             22
D17V3, multiclass
D17V4, multiclass
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  CLUS_1                            9                             17
  CLUS_2                            6                             32
  CLUS_3                           10                             19
D17V5, multiclass
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  CLUS_1                           12                             21
  CLUS_2                            8                             32
  CLUS_3                           13                             40
D17V6, multiclass
D17V7, multiclass
D17V8, multiclass
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            3                              9
  CLUS_3                            7                             12
D17V9, multiclass
D17V10, multiclass
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                           17                             46
  CLUS_3                           19                             40

Clustering(18) Variable = Amp Peak 18(17q12) mutation analysis
D18V1, multiclass
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  CLUS_1                          2                           23
  CLUS_2                          8                           12
  CLUS_3                         11                           13
D18V2, multiclass
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  CLUS_1                          6                           13
  CLUS_2                          4                           20
  CLUS_3                         11                           15
D18V3, multiclass
D18V4, multiclass
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  CLUS_1                          8                           18
  CLUS_2                          7                           31
  CLUS_3                          7                           22
D18V5, multiclass
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  CLUS_1                         13                           20
  CLUS_2                         11                           29
  CLUS_3                         11                           42
D18V6, multiclass
D18V7, multiclass
D18V8, multiclass
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  CLUS_1                          5                           14
  CLUS_2                          1                           11
  CLUS_3                          8                           11
D18V9, multiclass
D18V10, multiclass
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  CLUS_1                          5                           14
  CLUS_2                         18                           45
  CLUS_3                         14                           45

Clustering(19) Variable = Amp Peak 19(17q24.1) mutation analysis
D19V1, multiclass
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  CLUS_1                            4                             21
  CLUS_2                            6                             14
  CLUS_3                            9                             15
D19V2, multiclass
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            6                             18
  CLUS_3                            8                             18
D19V3, multiclass
D19V4, multiclass
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  CLUS_1                            8                             18
  CLUS_2                            4                             34
  CLUS_3                            6                             23
D19V5, multiclass
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  CLUS_1                           10                             23
  CLUS_2                            8                             32
  CLUS_3                           13                             40
D19V6, multiclass
D19V7, multiclass
D19V8, multiclass
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            1                             11
  CLUS_3                            7                             12
D19V9, multiclass
D19V10, multiclass
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                           16                             47
  CLUS_3                           11                             48

Clustering(20) Variable = Amp Peak 20(19p13.2) mutation analysis
D20V1, multiclass
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  CLUS_1                            2                             23
  CLUS_2                            4                             16
  CLUS_3                            9                             15
D20V2, multiclass
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                            1                             23
  CLUS_3                            6                             20
D20V3, multiclass
D20V4, multiclass
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  CLUS_1                            6                             20
  CLUS_2                            6                             32
  CLUS_3                            6                             23
D20V5, multiclass
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  CLUS_1                            9                             24
  CLUS_2                            6                             34
  CLUS_3                            9                             44
D20V6, multiclass
D20V7, multiclass
D20V8, multiclass
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                            1                             11
  CLUS_3                            5                             14
D20V9, multiclass
D20V10, multiclass
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                           13                             50
  CLUS_3                           11                             48

Clustering(21) Variable = Amp Peak 21(20q11.21) mutation analysis
D21V1, multiclass
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  CLUS_1                            22                               3
  CLUS_2                            14                               6
  CLUS_3                            23                               1
D21V2, multiclass
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  CLUS_1                            19                               0
  CLUS_2                            21                               3
  CLUS_3                            19                               7
D21V3, multiclass
D21V4, multiclass
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  CLUS_1                            26                               0
  CLUS_2                            35                               3
  CLUS_3                            23                               6
D21V5, multiclass
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  CLUS_1                            27                               6
  CLUS_2                            37                               3
  CLUS_3                            50                               3
D21V6, multiclass
D21V7, multiclass
D21V8, multiclass
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  CLUS_1                            16                               3
  CLUS_2                            11                               1
  CLUS_3                            19                               0
D21V9, multiclass
D21V10, multiclass
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  CLUS_1                            17                               2
  CLUS_2                            52                              11
  CLUS_3                            56                               3

Clustering(22) Variable = Amp Peak 22(20q11.23) mutation analysis
D22V1, multiclass
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  CLUS_1                            22                               3
  CLUS_2                            14                               6
  CLUS_3                            23                               1
D22V2, multiclass
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  CLUS_1                            19                               0
  CLUS_2                            21                               3
  CLUS_3                            19                               7
D22V3, multiclass
D22V4, multiclass
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  CLUS_1                            26                               0
  CLUS_2                            35                               3
  CLUS_3                            24                               5
D22V5, multiclass
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  CLUS_1                            27                               6
  CLUS_2                            37                               3
  CLUS_3                            50                               3
D22V6, multiclass
D22V7, multiclass
D22V8, multiclass
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  CLUS_1                            16                               3
  CLUS_2                            11                               1
  CLUS_3                            19                               0
D22V9, multiclass
D22V10, multiclass
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  CLUS_1                            18                               1
  CLUS_2                            52                              11
  CLUS_3                            56                               3

Clustering(23) Variable = Amp Peak 23(20q13.31) mutation analysis
D23V1, multiclass
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  CLUS_1                            23                               2
  CLUS_2                            14                               6
  CLUS_3                            23                               1
D23V2, multiclass
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  CLUS_1                            19                               0
  CLUS_2                            22                               2
  CLUS_3                            19                               7
D23V3, multiclass
D23V4, multiclass
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  CLUS_1                            26                               0
  CLUS_2                            35                               3
  CLUS_3                            24                               5
D23V5, multiclass
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  CLUS_1                            27                               6
  CLUS_2                            37                               3
  CLUS_3                            50                               3
D23V6, multiclass
D23V7, multiclass
D23V8, multiclass
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  CLUS_1                            16                               3
  CLUS_2                            11                               1
  CLUS_3                            19                               0
D23V9, multiclass
D23V10, multiclass
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  CLUS_1                            18                               1
  CLUS_2                            53                              10
  CLUS_3                            56                               3

Clustering(24) Variable = Amp Peak 24(Xp22.2) mutation analysis
D24V1, multiclass
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  CLUS_1                           3                            22
  CLUS_2                           1                            19
  CLUS_3                           8                            16
D24V2, multiclass
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           4                            20
  CLUS_3                           2                            24
D24V3, multiclass
D24V4, multiclass
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  CLUS_1                           6                            20
  CLUS_2                           6                            32
  CLUS_3                           8                            21
D24V5, multiclass
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  CLUS_1                           6                            27
  CLUS_2                          10                            30
  CLUS_3                          12                            41
D24V6, multiclass
D24V7, multiclass
D24V8, multiclass
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                           3                             9
  CLUS_3                           5                            14
D24V9, multiclass
D24V10, multiclass
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                          11                            52
  CLUS_3                          12                            47

Clustering(25) Variable = Amp Peak 25(Xq27.3) mutation analysis
D25V1, multiclass
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  CLUS_1                           6                            19
  CLUS_2                           4                            16
  CLUS_3                          11                            13
D25V2, multiclass
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  CLUS_1                           8                            11
  CLUS_2                           6                            18
  CLUS_3                           7                            19
D25V3, multiclass
D25V4, multiclass
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  CLUS_1                           8                            18
  CLUS_2                           6                            32
  CLUS_3                           2                            27
D25V5, multiclass
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  CLUS_1                           9                            24
  CLUS_2                           7                            33
  CLUS_3                          12                            41
D25V6, multiclass
D25V7, multiclass
D25V8, multiclass
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           2                            10
  CLUS_3                           4                            15
D25V9, multiclass
D25V10, multiclass
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                          18                            45
  CLUS_3                          11                            48

Clustering(26) Variable = Del Peak  1(1p36.11) mutation analysis
D26V1, multiclass
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  CLUS_1                           10                             15
  CLUS_2                            9                             11
  CLUS_3                           14                             10
D26V2, multiclass
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  CLUS_1                           12                              7
  CLUS_2                           11                             13
  CLUS_3                           10                             16
D26V3, multiclass
D26V4, multiclass
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  CLUS_1                           14                             12
  CLUS_2                           16                             22
  CLUS_3                            9                             20
D26V5, multiclass
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  CLUS_1                           15                             18
  CLUS_2                           15                             25
  CLUS_3                           23                             30
D26V6, multiclass
D26V7, multiclass
D26V8, multiclass
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            5                              7
  CLUS_3                            9                             10
D26V9, multiclass
D26V10, multiclass
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  CLUS_1                           10                              9
  CLUS_2                           28                             35
  CLUS_3                           25                             34

Clustering(27) Variable = Del Peak  2(1p33) mutation analysis
D27V1, multiclass
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  CLUS_1                         6                          19
  CLUS_2                         5                          15
  CLUS_3                         8                          16
D27V2, multiclass
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  CLUS_1                         8                          11
  CLUS_2                         6                          18
  CLUS_3                         5                          21
D27V3, multiclass
D27V4, multiclass
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  CLUS_1                        10                          16
  CLUS_2                        15                          23
  CLUS_3                         6                          23
D27V5, multiclass
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  CLUS_1                         9                          24
  CLUS_2                        11                          29
  CLUS_3                        17                          36
D27V6, multiclass
D27V7, multiclass
D27V8, multiclass
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  CLUS_1                         7                          12
  CLUS_2                         4                           8
  CLUS_3                         7                          12
D27V9, multiclass
D27V10, multiclass
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  CLUS_1                         8                          11
  CLUS_2                        15                          48
  CLUS_3                        21                          38

Clustering(28) Variable = Del Peak  3(1p13.2) mutation analysis
D28V1, multiclass
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  CLUS_1                           5                            20
  CLUS_2                           6                            14
  CLUS_3                           7                            17
D28V2, multiclass
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  CLUS_1                           7                            12
  CLUS_2                           5                            19
  CLUS_3                           6                            20
D28V3, multiclass
D28V4, multiclass
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  CLUS_1                           9                            17
  CLUS_2                          16                            22
  CLUS_3                           9                            20
D28V5, multiclass
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  CLUS_1                          13                            20
  CLUS_2                          11                            29
  CLUS_3                          16                            37
D28V6, multiclass
D28V7, multiclass
D28V8, multiclass
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  CLUS_1                           9                            10
  CLUS_2                           3                             9
  CLUS_3                           8                            11
D28V9, multiclass
D28V10, multiclass
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  CLUS_1                           8                            11
  CLUS_2                          14                            49
  CLUS_3                          22                            37

Clustering(29) Variable = Del Peak  4(2p12) mutation analysis
D29V1, multiclass
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  CLUS_1                         2                          23
  CLUS_2                         5                          15
  CLUS_3                         3                          21
D29V2, multiclass
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  CLUS_1                         2                          17
  CLUS_2                         2                          22
  CLUS_3                         6                          20
D29V3, multiclass
D29V4, multiclass
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  CLUS_1                         1                          25
  CLUS_2                         2                          36
  CLUS_3                         4                          25
D29V5, multiclass
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  CLUS_1                         6                          27
  CLUS_2                         4                          36
  CLUS_3                         4                          49
D29V6, multiclass
D29V7, multiclass
D29V8, multiclass
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  CLUS_1                         2                          17
  CLUS_2                         1                          11
  CLUS_3                         1                          18
D29V9, multiclass
D29V10, multiclass
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  CLUS_1                         1                          18
  CLUS_2                         9                          54
  CLUS_3                         6                          53

Clustering(30) Variable = Del Peak  5(3p14.2) mutation analysis
D30V1, multiclass
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CLUS_1                           5                            20
  CLUS_2                           5                            15
  CLUS_3                           3                            21
D30V2, multiclass
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                           4                            20
  CLUS_3                           6                            20
D30V3, multiclass
D30V4, multiclass
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CLUS_1                           4                            22
  CLUS_2                           7                            31
  CLUS_3                           5                            24
D30V5, multiclass
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CLUS_1                           9                            24
  CLUS_2                           5                            35
  CLUS_3                           8                            45
D30V6, multiclass
D30V7, multiclass
D30V8, multiclass
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CLUS_1                           2                            17
  CLUS_2                           4                             8
  CLUS_3                           3                            16
D30V9, multiclass
D30V10, multiclass
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  CLUS_1                           4                            15
  CLUS_2                          13                            50
  CLUS_3                          12                            47

Clustering(31) Variable = Del Peak  6(3q26.31) mutation analysis
D31V1, multiclass
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  CLUS_1                            3                             22
  CLUS_2                            3                             17
  CLUS_3                            3                             21
D31V2, multiclass
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                            3                             21
  CLUS_3                            3                             23
D31V3, multiclass
D31V4, multiclass
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  CLUS_1                            2                             24
  CLUS_2                            4                             34
  CLUS_3                            3                             26
D31V5, multiclass
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  CLUS_1                            4                             29
  CLUS_2                            4                             36
  CLUS_3                            4                             49
D31V6, multiclass
D31V7, multiclass
D31V8, multiclass
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            1                             11
  CLUS_3                            2                             17
D31V9, multiclass
D31V10, multiclass
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            8                             55
  CLUS_3                            6                             53

Clustering(32) Variable = Del Peak  7(4p13) mutation analysis
D32V1, multiclass
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  CLUS_1                         8                          17
  CLUS_2                         8                          12
  CLUS_3                         9                          15
D32V2, multiclass
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  CLUS_1                         8                          11
  CLUS_2                         7                          17
  CLUS_3                        10                          16
D32V3, multiclass
D32V4, multiclass
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  CLUS_1                        14                          12
  CLUS_2                        11                          27
  CLUS_3                         8                          21
D32V5, multiclass
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  CLUS_1                        10                          23
  CLUS_2                        15                          25
  CLUS_3                        17                          36
D32V6, multiclass
D32V7, multiclass
D32V8, multiclass
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  CLUS_1                         9                          10
  CLUS_2                         6                           6
  CLUS_3                         5                          14
D32V9, multiclass
D32V10, multiclass
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  CLUS_1                        12                           7
  CLUS_2                        21                          42
  CLUS_3                        21                          38

Clustering(33) Variable = Del Peak  8(4q22.1) mutation analysis
D33V1, multiclass
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CLUS_1                           9                            16
  CLUS_2                           9                            11
  CLUS_3                          10                            14
D33V2, multiclass
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                           8                            16
  CLUS_3                          10                            16
D33V3, multiclass
D33V4, multiclass
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CLUS_1                          16                            10
  CLUS_2                          16                            22
  CLUS_3                          13                            16
D33V5, multiclass
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CLUS_1                          15                            18
  CLUS_2                          18                            22
  CLUS_3                          20                            33
D33V6, multiclass
D33V7, multiclass
D33V8, multiclass
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CLUS_1                          11                             8
  CLUS_2                           9                             3
  CLUS_3                           6                            13
D33V9, multiclass
D33V10, multiclass
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  CLUS_1                          13                             6
  CLUS_2                          25                            38
  CLUS_3                          29                            30

Clustering(34) Variable = Del Peak  9(4q35.1) mutation analysis
D34V1, multiclass
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  CLUS_1                           8                            17
  CLUS_2                          10                            10
  CLUS_3                           8                            16
D34V2, multiclass
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  CLUS_1                           8                            11
  CLUS_2                           7                            17
  CLUS_3                          11                            15
D34V3, multiclass
D34V4, multiclass
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  CLUS_1                          17                             9
  CLUS_2                          15                            23
  CLUS_3                          14                            15
D34V5, multiclass
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  CLUS_1                          15                            18
  CLUS_2                          19                            21
  CLUS_3                          19                            34
D34V6, multiclass
D34V7, multiclass
D34V8, multiclass
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  CLUS_1                          12                             7
  CLUS_2                           9                             3
  CLUS_3                           6                            13
D34V9, multiclass
D34V10, multiclass
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  CLUS_1                          13                             6
  CLUS_2                          23                            40
  CLUS_3                          30                            29

Clustering(35) Variable = Del Peak 10(5q11.2) mutation analysis
D35V1, multiclass
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  CLUS_1                           3                            22
  CLUS_2                           5                            15
  CLUS_3                           8                            16
D35V2, multiclass
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  CLUS_1                           8                            11
  CLUS_2                           3                            21
  CLUS_3                           5                            21
D35V3, multiclass
D35V4, multiclass
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  CLUS_1                          16                            10
  CLUS_2                           7                            31
  CLUS_3                          11                            18
D35V5, multiclass
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  CLUS_1                           9                            24
  CLUS_2                          12                            28
  CLUS_3                          17                            36
D35V6, multiclass
D35V7, multiclass
D35V8, multiclass
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  CLUS_1                           7                            12
  CLUS_2                           5                             7
  CLUS_3                           6                            13
D35V9, multiclass
D35V10, multiclass
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                          14                            49
  CLUS_3                          20                            39

Clustering(36) Variable = Del Peak 11(5q22.2) mutation analysis
D36V1, multiclass
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  CLUS_1                           5                            20
  CLUS_2                           7                            13
  CLUS_3                           9                            15
D36V2, multiclass
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  CLUS_1                           9                            10
  CLUS_2                           5                            19
  CLUS_3                           7                            19
D36V3, multiclass
D36V4, multiclass
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  CLUS_1                          13                            13
  CLUS_2                          12                            26
  CLUS_3                          10                            19
D36V5, multiclass
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  CLUS_1                          10                            23
  CLUS_2                          16                            24
  CLUS_3                          18                            35
D36V6, multiclass
D36V7, multiclass
D36V8, multiclass
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  CLUS_1                           5                            14
  CLUS_2                           5                             7
  CLUS_3                           5                            14
D36V9, multiclass
D36V10, multiclass
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                          19                            44
  CLUS_3                          22                            37

Clustering(37) Variable = Del Peak 12(6p25.3) mutation analysis
D37V1, multiclass
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  CLUS_1                           4                            21
  CLUS_2                           3                            17
  CLUS_3                           3                            21
D37V2, multiclass
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                           3                            21
  CLUS_3                           4                            22
D37V3, multiclass
D37V4, multiclass
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  CLUS_1                           0                            26
  CLUS_2                           8                            30
  CLUS_3                           6                            23
D37V5, multiclass
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  CLUS_1                           5                            28
  CLUS_2                           4                            36
  CLUS_3                           9                            44
D37V6, multiclass
D37V7, multiclass
D37V8, multiclass
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                           3                             9
  CLUS_3                           2                            17
D37V9, multiclass
D37V10, multiclass
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  CLUS_1                           3                            16
  CLUS_2                           8                            55
  CLUS_3                          12                            47

Clustering(38) Variable = Del Peak 13(6q26) mutation analysis
D38V1, multiclass
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CLUS_1                         4                          21
  CLUS_2                         8                          12
  CLUS_3                         6                          18
D38V2, multiclass
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CLUS_1                         4                          15
  CLUS_2                         3                          21
  CLUS_3                        11                          15
D38V3, multiclass
D38V4, multiclass
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CLUS_1                         2                          24
  CLUS_2                         6                          32
  CLUS_3                         4                          25
D38V5, multiclass
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CLUS_1                        10                          23
  CLUS_2                         4                          36
  CLUS_3                         9                          44
D38V6, multiclass
D38V7, multiclass
D38V8, multiclass
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CLUS_1                         4                          15
  CLUS_2                         3                           9
  CLUS_3                         2                          17
D38V9, multiclass
D38V10, multiclass
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  CLUS_1                         1                          18
  CLUS_2                        18                          45
  CLUS_3                        10                          49

Clustering(39) Variable = Del Peak 14(7q31.1) mutation analysis
D39V1, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(7Q31.1) MUTATED"
clus
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            2                            67 
                   TCGA-AF-2689                    TCGA-AF-2691 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2692                    TCGA-AF-3400 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-3913                    TCGA-AG-3574 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3575                    TCGA-AG-3578 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3580                    TCGA-AG-3581 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3582                    TCGA-AG-3583 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3584                    TCGA-AG-3586 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3587                    TCGA-AG-3593 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3594                    TCGA-AG-3598 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3599                    TCGA-AG-3601 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3602                    TCGA-AG-3605 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3608                    TCGA-AG-3609 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3611                    TCGA-AG-3612 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3726                    TCGA-AG-3727 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3728                    TCGA-AG-3878 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3881                    TCGA-AG-3882 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3883                    TCGA-AG-3885 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3887                    TCGA-AG-3890 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3892                    TCGA-AG-3893 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3894                    TCGA-AG-3896 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3898                    TCGA-AG-3901 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3902                    TCGA-AG-3909 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3999                    TCGA-AG-4001 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-4005                    TCGA-AG-4007 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-4008                    TCGA-AG-4015 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A002                    TCGA-AG-A00C 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A00H                    TCGA-AG-A00Y 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A011                    TCGA-AG-A014 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A015                    TCGA-AG-A016 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A01J                    TCGA-AG-A01L 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A01N                    TCGA-AG-A023 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A025                    TCGA-AG-A026 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A02G                    TCGA-AG-A02X 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A032 
"DEL PEAK 14(7Q31.1) WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(7Q31.1) MUTATED"
clus
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            2                            67 
                   TCGA-AF-2689                    TCGA-AF-2691 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2692                    TCGA-AF-3400 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-3913                    TCGA-AG-3574 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3575                    TCGA-AG-3578 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3580                    TCGA-AG-3581 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3582                    TCGA-AG-3583 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3584                    TCGA-AG-3586 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3587                    TCGA-AG-3593 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3594                    TCGA-AG-3598 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3599                    TCGA-AG-3601 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3602                    TCGA-AG-3605 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3608                    TCGA-AG-3609 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3611                    TCGA-AG-3612 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3726                    TCGA-AG-3727 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3728                    TCGA-AG-3878 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3881                    TCGA-AG-3882 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3883                    TCGA-AG-3885 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3887                    TCGA-AG-3890 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3892                    TCGA-AG-3893 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3894                    TCGA-AG-3896 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3898                    TCGA-AG-3901 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3902                    TCGA-AG-3909 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3999                    TCGA-AG-4001 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-4005                    TCGA-AG-4007 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-4008                    TCGA-AG-4015 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A002                    TCGA-AG-A00C 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A00H                    TCGA-AG-A00Y 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A011                    TCGA-AG-A014 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A015                    TCGA-AG-A016 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A01J                    TCGA-AG-A01L 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A01N                    TCGA-AG-A023 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A025                    TCGA-AG-A026 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A02G                    TCGA-AG-A02X 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A032 
"DEL PEAK 14(7Q31.1) WILD-TYPE" 
D39V3, multiclass
D39V4, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(7Q31.1) MUTATED"
clus
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            2                            91 
                   TCGA-AF-2687                    TCGA-AF-2690 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2693                    TCGA-AF-3911 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-4110                    TCGA-AF-6136 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-6655                    TCGA-AF-6672 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3592                    TCGA-AG-3725 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3731                    TCGA-AG-3732 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3742                    TCGA-AG-4021 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-4022                    TCGA-AG-A01W 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A01Y                    TCGA-AG-A020 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-A026                    TCGA-AG-A02N 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6544                    TCGA-AH-6547 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6643                    TCGA-AH-6644 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6897                    TCGA-AH-6903 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-BM-6198                    TCGA-CI-6619 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6620                    TCGA-CI-6621 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6622                    TCGA-CI-6623 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6624                    TCGA-CL-4957 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CL-5917                    TCGA-CL-5918 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-4745                    TCGA-DC-4749 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-5337                    TCGA-DC-5869 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6154                    TCGA-DC-6155 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6156                    TCGA-DC-6157 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6158                    TCGA-DC-6160 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6681                    TCGA-DC-6683 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DT-5265                    TCGA-DY-A0XA 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DC                    TCGA-DY-A1DD 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DE                    TCGA-DY-A1DF 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DG                    TCGA-DY-A1H8 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EF-5830                    TCGA-EF-5831 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6506                    TCGA-EI-6507 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6508                    TCGA-EI-6509 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6510                    TCGA-EI-6511 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6512                    TCGA-EI-6513 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6514                    TCGA-EI-6881 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6882                    TCGA-EI-6883 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6884                    TCGA-EI-6885 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6917                    TCGA-EI-7002 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-7004                    TCGA-F5-6464 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6465                    TCGA-F5-6571 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6702                    TCGA-F5-6810 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6811                    TCGA-F5-6812 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6813                    TCGA-F5-6814 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6861                    TCGA-F5-6863 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6864                    TCGA-G5-6233 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-G5-6235                    TCGA-G5-6572 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-G5-6641 
"DEL PEAK 14(7Q31.1) WILD-TYPE" 
D39V5, multiclass
        clus
vv       DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  CLUS_1                           1                            32
  CLUS_2                           1                            39
  CLUS_3                           2                            51
D39V6, multiclass
D39V7, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(7Q31.1) MUTATED"
clus
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            2                            48 
                   TCGA-AF-2687                    TCGA-AF-2690 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2693                    TCGA-AF-3911 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-4110                    TCGA-AF-5654 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-6136                    TCGA-AG-3732 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3742                    TCGA-AG-4022 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6643                    TCGA-AH-6644 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6897                    TCGA-CI-6623 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6624                    TCGA-CL-5917 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CL-5918                    TCGA-DC-5337 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-5869                    TCGA-DC-6154 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6156                    TCGA-DC-6157 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6158                    TCGA-DC-6160 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6683                    TCGA-DT-5265 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A0XA                    TCGA-DY-A1DE 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DF                    TCGA-DY-A1H8 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EF-5830                    TCGA-EI-6883 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6884                    TCGA-EI-6885 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6917                    TCGA-EI-7002 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-7004                    TCGA-F5-6571 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6702                    TCGA-F5-6810 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6811                    TCGA-F5-6812 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6813                    TCGA-F5-6814 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6861                    TCGA-F5-6863 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6864                    TCGA-G5-6235 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
D39V8, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(7Q31.1) MUTATED"
clus
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            2                            48 
                   TCGA-AF-2687                    TCGA-AF-2690 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2693                    TCGA-AF-3911 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-4110                    TCGA-AF-5654 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-6136                    TCGA-AG-3732 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AG-3742                    TCGA-AG-4022 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6643                    TCGA-AH-6644 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6897                    TCGA-CI-6623 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6624                    TCGA-CL-5917 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CL-5918                    TCGA-DC-5337 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-5869                    TCGA-DC-6154 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6156                    TCGA-DC-6157 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6158                    TCGA-DC-6160 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6683                    TCGA-DT-5265 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A0XA                    TCGA-DY-A1DE 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DF                    TCGA-DY-A1H8 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EF-5830                    TCGA-EI-6883 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6884                    TCGA-EI-6885 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6917                    TCGA-EI-7002 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-7004                    TCGA-F5-6571 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6702                    TCGA-F5-6810 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6811                    TCGA-F5-6812 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6813                    TCGA-F5-6814 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6861                    TCGA-F5-6863 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6864                    TCGA-G5-6235 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
D39V9, multiclass
D39V10, multiclass
        clus
vv       DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  CLUS_1                           0                            19
  CLUS_2                           2                            61
  CLUS_3                           2                            57

Clustering(40) Variable = Del Peak 15(8p23.2) mutation analysis
D40V1, multiclass
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  CLUS_1                          13                            12
  CLUS_2                          13                             7
  CLUS_3                          19                             5
D40V2, multiclass
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  CLUS_1                          16                             3
  CLUS_2                          15                             9
  CLUS_3                          14                            12
D40V3, multiclass
D40V4, multiclass
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  CLUS_1                          19                             7
  CLUS_2                          22                            16
  CLUS_3                          15                            14
D40V5, multiclass
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  CLUS_1                          21                            12
  CLUS_2                          25                            15
  CLUS_3                          33                            20
D40V6, multiclass
D40V7, multiclass
D40V8, multiclass
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  CLUS_1                          15                             4
  CLUS_2                           8                             4
  CLUS_3                          10                             9
D40V9, multiclass
D40V10, multiclass
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  CLUS_1                          13                             6
  CLUS_2                          39                            24
  CLUS_3                          36                            23

Clustering(41) Variable = Del Peak 16(8p11.21) mutation analysis
D41V1, multiclass
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  CLUS_1                            6                             19
  CLUS_2                            6                             14
  CLUS_3                            2                             22
D41V2, multiclass
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            5                             19
  CLUS_3                            7                             19
D41V3, multiclass
D41V4, multiclass
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  CLUS_1                            5                             21
  CLUS_2                            2                             36
  CLUS_3                            3                             26
D41V5, multiclass
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  CLUS_1                            8                             25
  CLUS_2                            3                             37
  CLUS_3                            6                             47
D41V6, multiclass
D41V7, multiclass
D41V8, multiclass
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            0                             12
  CLUS_3                            3                             16
D41V9, multiclass
D41V10, multiclass
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                           15                             48
  CLUS_3                            6                             53

Clustering(42) Variable = Del Peak 17(10q21.1) mutation analysis
D42V1, multiclass
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  CLUS_1                            9                             16
  CLUS_2                            6                             14
  CLUS_3                            3                             21
D42V2, multiclass
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                            9                             15
  CLUS_3                            6                             20
D42V3, multiclass
D42V4, multiclass
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  CLUS_1                            8                             18
  CLUS_2                            7                             31
  CLUS_3                            5                             24
D42V5, multiclass
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  CLUS_1                            4                             29
  CLUS_2                            6                             34
  CLUS_3                           17                             36
D42V6, multiclass
D42V7, multiclass
D42V8, multiclass
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            4                              8
  CLUS_3                            3                             16
D42V9, multiclass
D42V10, multiclass
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                           15                             48
  CLUS_3                           13                             46

Clustering(43) Variable = Del Peak 18(10q25.2) mutation analysis
D43V1, multiclass
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  CLUS_1                            9                             16
  CLUS_2                            6                             14
  CLUS_3                            5                             19
D43V2, multiclass
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            8                             16
  CLUS_3                            7                             19
D43V3, multiclass
D43V4, multiclass
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  CLUS_1                            9                             17
  CLUS_2                            9                             29
  CLUS_3                            9                             20
D43V5, multiclass
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  CLUS_1                           11                             22
  CLUS_2                            9                             31
  CLUS_3                           18                             35
D43V6, multiclass
D43V7, multiclass
D43V8, multiclass
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            4                              8
  CLUS_3                            5                             14
D43V9, multiclass
D43V10, multiclass
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  CLUS_1                            7                             12
  CLUS_2                           19                             44
  CLUS_3                           16                             43

Clustering(44) Variable = Del Peak 19(11q22.3) mutation analysis
D44V1, multiclass
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  CLUS_1                            6                             19
  CLUS_2                            8                             12
  CLUS_3                            0                             24
D44V2, multiclass
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  CLUS_1                            0                             19
  CLUS_2                            5                             19
  CLUS_3                            9                             17
D44V3, multiclass
D44V4, multiclass
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  CLUS_1                            2                             24
  CLUS_2                           11                             27
  CLUS_3                           10                             19
D44V5, multiclass
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  CLUS_1                            6                             27
  CLUS_2                            9                             31
  CLUS_3                           13                             40
D44V6, multiclass
D44V7, multiclass
D44V8, multiclass
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            7                              5
  CLUS_3                            0                             19
D44V9, multiclass
D44V10, multiclass
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                           16                             47
  CLUS_3                           16                             43

Clustering(45) Variable = Del Peak 20(12p13.1) mutation analysis
D45V1, multiclass
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  CLUS_1                            4                             21
  CLUS_2                            3                             17
  CLUS_3                            4                             20
D45V2, multiclass
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            4                             20
  CLUS_3                            3                             23
D45V3, multiclass
D45V4, multiclass
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  CLUS_1                            4                             22
  CLUS_2                            9                             29
  CLUS_3                           10                             19
D45V5, multiclass
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  CLUS_1                            6                             27
  CLUS_2                            7                             33
  CLUS_3                           14                             39
D45V6, multiclass
D45V7, multiclass
D45V8, multiclass
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                            5                              7
  CLUS_3                            0                             19
D45V9, multiclass
D45V10, multiclass
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  CLUS_1                            7                             12
  CLUS_2                           11                             52
  CLUS_3                           14                             45

Clustering(46) Variable = Del Peak 21(12q21.33) mutation analysis
D46V1, multiclass
        clus
vv       DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE
  CLUS_1                             3                              22
  CLUS_2                             4                              16
  CLUS_3                             5                              19
D46V2, multiclass
        clus
vv       DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE
  CLUS_1                             4                              15
  CLUS_2                             4                              20
  CLUS_3                             4                              22
D46V3, multiclass
D46V4, multiclass
        clus
vv       DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE
  CLUS_1                             3                              23
  CLUS_2                             7                              31
  CLUS_3                             6                              23
D46V5, multiclass
        clus
vv       DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE
  CLUS_1                             6                              27
  CLUS_2                             5                              35
  CLUS_3                            11                              42
D46V6, multiclass
D46V7, multiclass
D46V8, multiclass
        clus
vv       DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE
  CLUS_1                             4                              15
  CLUS_2                             5                               7
  CLUS_3                             1                              18
D46V9, multiclass
D46V10, multiclass
        clus
vv       DEL PEAK 21(12Q21.33) MUTATED DEL PEAK 21(12Q21.33) WILD-TYPE
  CLUS_1                             3                              16
  CLUS_2                             7                              56
  CLUS_3                            13                              46

Clustering(47) Variable = Del Peak 22(14q11.2) mutation analysis
D47V1, multiclass
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  CLUS_1                           10                             15
  CLUS_2                            7                             13
  CLUS_3                           10                             14
D47V2, multiclass
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  CLUS_1                           10                              9
  CLUS_2                            9                             15
  CLUS_3                            8                             18
D47V3, multiclass
D47V4, multiclass
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  CLUS_1                           12                             14
  CLUS_2                           17                             21
  CLUS_3                           12                             17
D47V5, multiclass
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  CLUS_1                           15                             18
  CLUS_2                           15                             25
  CLUS_3                           23                             30
D47V6, multiclass
D47V7, multiclass
D47V8, multiclass
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            7                              5
  CLUS_3                            9                             10
D47V9, multiclass
D47V10, multiclass
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  CLUS_1                           10                              9
  CLUS_2                           21                             42
  CLUS_3                           29                             30

Clustering(48) Variable = Del Peak 23(14q31.1) mutation analysis
D48V1, multiclass
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  CLUS_1                           10                             15
  CLUS_2                            7                             13
  CLUS_3                           10                             14
D48V2, multiclass
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  CLUS_1                           10                              9
  CLUS_2                            8                             16
  CLUS_3                            9                             17
D48V3, multiclass
D48V4, multiclass
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  CLUS_1                           12                             14
  CLUS_2                           18                             20
  CLUS_3                           13                             16
D48V5, multiclass
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  CLUS_1                           17                             16
  CLUS_2                           17                             23
  CLUS_3                           22                             31
D48V6, multiclass
D48V7, multiclass
D48V8, multiclass
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            6                              6
  CLUS_3                           10                              9
D48V9, multiclass
D48V10, multiclass
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  CLUS_1                           10                              9
  CLUS_2                           22                             41
  CLUS_3                           29                             30

Clustering(49) Variable = Del Peak 24(15q22.33) mutation analysis
D49V1, multiclass
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  CLUS_1                            10                              15
  CLUS_2                            11                               9
  CLUS_3                            11                              13
D49V2, multiclass
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  CLUS_1                            11                               8
  CLUS_2                             9                              15
  CLUS_3                            12                              14
D49V3, multiclass
D49V4, multiclass
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  CLUS_1                            14                              12
  CLUS_2                            16                              22
  CLUS_3                            13                              16
D49V5, multiclass
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  CLUS_1                            11                              22
  CLUS_2                            19                              21
  CLUS_3                            28                              25
D49V6, multiclass
D49V7, multiclass
D49V8, multiclass
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  CLUS_1                            10                               9
  CLUS_2                             4                               8
  CLUS_3                            11                               8
D49V9, multiclass
D49V10, multiclass
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  CLUS_1                             9                              10
  CLUS_2                            27                              36
  CLUS_3                            29                              30

Clustering(50) Variable = Del Peak 25(16p13.3) mutation analysis
D50V1, multiclass
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  CLUS_1                            2                             23
  CLUS_2                            3                             17
  CLUS_3                            2                             22
D50V2, multiclass
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            2                             22
  CLUS_3                            4                             22
D50V3, multiclass
D50V4, multiclass
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  CLUS_1                            0                             26
  CLUS_2                            1                             37
  CLUS_3                            5                             24
D50V5, multiclass
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  CLUS_1                            4                             29
  CLUS_2                            3                             37
  CLUS_3                            4                             49
D50V6, multiclass
D50V7, multiclass
D50V8, multiclass
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            1                             11
  CLUS_3                            2                             17
D50V9, multiclass
D50V10, multiclass
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  CLUS_1                            0                             19
  CLUS_2                            7                             56
  CLUS_3                            4                             55

Clustering(51) Variable = Del Peak 26(16q23.1) mutation analysis
D51V1, multiclass
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  CLUS_1                            1                             24
  CLUS_2                            5                             15
  CLUS_3                            2                             22
D51V2, multiclass
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            1                             23
  CLUS_3                            6                             20
D51V3, multiclass
D51V4, multiclass
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  CLUS_1                            2                             24
  CLUS_2                            5                             33
  CLUS_3                            8                             21
D51V5, multiclass
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  CLUS_1                            6                             27
  CLUS_2                            4                             36
  CLUS_3                            6                             47
D51V6, multiclass
D51V7, multiclass
D51V8, multiclass
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            2                             10
  CLUS_3                            4                             15
D51V9, multiclass
D51V10, multiclass
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  CLUS_1                            0                             19
  CLUS_2                            8                             55
  CLUS_3                           11                             48

Clustering(52) Variable = Del Peak 27(17p12) mutation analysis
D52V1, multiclass
        clus
vv       DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE
  CLUS_1                         14                           11
  CLUS_2                         13                            7
  CLUS_3                         20                            4
D52V2, multiclass
        clus
vv       DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE
  CLUS_1                         15                            4
  CLUS_2                         14                           10
  CLUS_3                         18                            8
D52V3, multiclass
D52V4, multiclass
        clus
vv       DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE
  CLUS_1                         17                            9
  CLUS_2                         24                           14
  CLUS_3                         23                            6
D52V5, multiclass
        clus
vv       DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE
  CLUS_1                         25                            8
  CLUS_2                         28                           12
  CLUS_3                         34                           19
D52V6, multiclass
D52V7, multiclass
D52V8, multiclass
        clus
vv       DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE
  CLUS_1                         16                            3
  CLUS_2                         10                            2
  CLUS_3                          9                           10
D52V9, multiclass
D52V10, multiclass
        clus
vv       DEL PEAK 27(17P12) MUTATED DEL PEAK 27(17P12) WILD-TYPE
  CLUS_1                         15                            4
  CLUS_2                         40                           23
  CLUS_3                         41                           18

Clustering(53) Variable = Del Peak 28(17p11.2) mutation analysis
D53V1, multiclass
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  CLUS_1                           14                             11
  CLUS_2                           13                              7
  CLUS_3                           19                              5
D53V2, multiclass
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  CLUS_1                           14                              5
  CLUS_2                           14                             10
  CLUS_3                           18                              8
D53V3, multiclass
D53V4, multiclass
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  CLUS_1                           15                             11
  CLUS_2                           22                             16
  CLUS_3                           20                              9
D53V5, multiclass
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  CLUS_1                           21                             12
  CLUS_2                           24                             16
  CLUS_3                           34                             19
D53V6, multiclass
D53V7, multiclass
D53V8, multiclass
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  CLUS_1                           12                              7
  CLUS_2                           10                              2
  CLUS_3                            8                             11
D53V9, multiclass
D53V10, multiclass
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  CLUS_1                           13                              6
  CLUS_2                           39                             24
  CLUS_3                           37                             22

Clustering(54) Variable = Del Peak 29(17q25.3) mutation analysis
D54V1, multiclass
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CLUS_1                            4                             21
  CLUS_2                            1                             19
  CLUS_3                            2                             22
D54V2, multiclass
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CLUS_1                            1                             18
  CLUS_2                            4                             20
  CLUS_3                            2                             24
D54V3, multiclass
D54V4, multiclass
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CLUS_1                            1                             25
  CLUS_2                            6                             32
  CLUS_3                           11                             18
D54V5, multiclass
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CLUS_1                            3                             30
  CLUS_2                            8                             32
  CLUS_3                            9                             44
D54V6, multiclass
D54V7, multiclass
D54V8, multiclass
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CLUS_1                            5                             14
  CLUS_2                            4                              8
  CLUS_3                            0                             19
D54V9, multiclass
D54V10, multiclass
        clus
vv       DEL PEAK 29(17Q25.3) MUTATED DEL PEAK 29(17Q25.3) WILD-TYPE
  CLUS_1                            2                             17
  CLUS_2                            6                             57
  CLUS_3                           13                             46

Clustering(55) Variable = Del Peak 30(18q21.2) mutation analysis
D55V1, multiclass
        clus
vv       DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CLUS_1                           19                              6
  CLUS_2                           18                              2
  CLUS_3                           23                              1
D55V2, multiclass
        clus
vv       DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CLUS_1                           19                              0
  CLUS_2                           19                              5
  CLUS_3                           22                              4
D55V3, multiclass
D55V4, multiclass
        clus
vv       DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CLUS_1                           26                              0
  CLUS_2                           32                              6
  CLUS_3                           26                              3
D55V5, multiclass
        clus
vv       DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CLUS_1                           29                              4
  CLUS_2                           35                              5
  CLUS_3                           47                              6
D55V6, multiclass
D55V7, multiclass
D55V8, multiclass
        clus
vv       DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CLUS_1                           17                              2
  CLUS_2                           12                              0
  CLUS_3                           16                              3
D55V9, multiclass
D55V10, multiclass
        clus
vv       DEL PEAK 30(18Q21.2) MUTATED DEL PEAK 30(18Q21.2) WILD-TYPE
  CLUS_1                           18                              1
  CLUS_2                           53                             10
  CLUS_3                           55                              4

Clustering(56) Variable = Del Peak 31(18q22.1) mutation analysis
D56V1, multiclass
        clus
vv       DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE
  CLUS_1                           18                              7
  CLUS_2                           18                              2
  CLUS_3                           23                              1
D56V2, multiclass
        clus
vv       DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE
  CLUS_1                           19                              0
  CLUS_2                           18                              6
  CLUS_3                           22                              4
D56V3, multiclass
D56V4, multiclass
        clus
vv       DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE
  CLUS_1                           26                              0
  CLUS_2                           30                              8
  CLUS_3                           24                              5
D56V5, multiclass
        clus
vv       DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE
  CLUS_1                           27                              6
  CLUS_2                           34                              6
  CLUS_3                           46                              7
D56V6, multiclass
D56V7, multiclass
D56V8, multiclass
        clus
vv       DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE
  CLUS_1                           16                              3
  CLUS_2                           12                              0
  CLUS_3                           16                              3
D56V9, multiclass
D56V10, multiclass
        clus
vv       DEL PEAK 31(18Q22.1) MUTATED DEL PEAK 31(18Q22.1) WILD-TYPE
  CLUS_1                           17                              2
  CLUS_2                           52                             11
  CLUS_3                           53                              6

Clustering(57) Variable = Del Peak 32(19p13.3) mutation analysis
D57V1, multiclass
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  CLUS_1                            2                             23
  CLUS_2                            5                             15
  CLUS_3                            6                             18
D57V2, multiclass
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            3                             21
  CLUS_3                            6                             20
D57V3, multiclass
D57V4, multiclass
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  CLUS_1                           12                             14
  CLUS_2                            7                             31
  CLUS_3                            6                             23
D57V5, multiclass
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  CLUS_1                            7                             26
  CLUS_2                            8                             32
  CLUS_3                           13                             40
D57V6, multiclass
D57V7, multiclass
D57V8, multiclass
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                            4                              8
  CLUS_3                            1                             18
D57V9, multiclass
D57V10, multiclass
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  CLUS_1                           10                              9
  CLUS_2                           11                             52
  CLUS_3                           15                             44

Clustering(58) Variable = Del Peak 33(20p12.1) mutation analysis
D58V1, multiclass
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CLUS_1                            9                             16
  CLUS_2                            9                             11
  CLUS_3                           12                             12
D58V2, multiclass
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                           10                             14
  CLUS_3                           11                             15
D58V3, multiclass
D58V4, multiclass
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CLUS_1                            9                             17
  CLUS_2                           11                             27
  CLUS_3                           11                             18
D58V5, multiclass
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CLUS_1                           13                             20
  CLUS_2                           18                             22
  CLUS_3                           18                             35
D58V6, multiclass
D58V7, multiclass
D58V8, multiclass
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            5                              7
  CLUS_3                            7                             12
D58V9, multiclass
D58V10, multiclass
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                           27                             36
  CLUS_3                           17                             42

Clustering(59) Variable = Del Peak 34(20p12.1) mutation analysis
D59V1, multiclass
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  CLUS_1                            9                             16
  CLUS_2                            9                             11
  CLUS_3                           12                             12
D59V2, multiclass
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                           10                             14
  CLUS_3                           11                             15
D59V3, multiclass
D59V4, multiclass
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  CLUS_1                            9                             17
  CLUS_2                           11                             27
  CLUS_3                           11                             18
D59V5, multiclass
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  CLUS_1                           13                             20
  CLUS_2                           18                             22
  CLUS_3                           18                             35
D59V6, multiclass
D59V7, multiclass
D59V8, multiclass
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            5                              7
  CLUS_3                            7                             12
D59V9, multiclass
D59V10, multiclass
        clus
vv       DEL PEAK 34(20P12.1) MUTATED DEL PEAK 34(20P12.1) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                           27                             36
  CLUS_3                           17                             42

Clustering(60) Variable = Del Peak 35(21q11.2) mutation analysis
D60V1, multiclass
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  CLUS_1                            7                             18
  CLUS_2                            6                             14
  CLUS_3                           11                             13
D60V2, multiclass
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            6                             18
  CLUS_3                            9                             17
D60V3, multiclass
D60V4, multiclass
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  CLUS_1                           13                             13
  CLUS_2                           18                             20
  CLUS_3                           16                             13
D60V5, multiclass
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  CLUS_1                           14                             19
  CLUS_2                           19                             21
  CLUS_3                           24                             29
D60V6, multiclass
D60V7, multiclass
D60V8, multiclass
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            6                              6
  CLUS_3                            8                             11
D60V9, multiclass
D60V10, multiclass
        clus
vv       DEL PEAK 35(21Q11.2) MUTATED DEL PEAK 35(21Q11.2) WILD-TYPE
  CLUS_1                           11                              8
  CLUS_2                           26                             37
  CLUS_3                           28                             31

Clustering(61) Variable = Del Peak 36(22q13.31) mutation analysis
D61V1, multiclass
        clus
vv       DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE
  CLUS_1                             9                              16
  CLUS_2                             8                              12
  CLUS_3                             9                              15
D61V2, multiclass
        clus
vv       DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE
  CLUS_1                             8                              11
  CLUS_2                             8                              16
  CLUS_3                            10                              16
D61V3, multiclass
D61V4, multiclass
        clus
vv       DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE
  CLUS_1                            10                              16
  CLUS_2                            18                              20
  CLUS_3                            13                              16
D61V5, multiclass
        clus
vv       DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE
  CLUS_1                            12                              21
  CLUS_2                            15                              25
  CLUS_3                            25                              28
D61V6, multiclass
D61V7, multiclass
D61V8, multiclass
        clus
vv       DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE
  CLUS_1                             6                              13
  CLUS_2                             7                               5
  CLUS_3                             5                              14
D61V9, multiclass
D61V10, multiclass
        clus
vv       DEL PEAK 36(22Q13.31) MUTATED DEL PEAK 36(22Q13.31) WILD-TYPE
  CLUS_1                            10                               9
  CLUS_2                            23                              40
  CLUS_3                            28                              31

Clustering(62) Variable = Del Peak 37(Xp22.33) mutation analysis
D62V1, multiclass
        clus
vv       DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE
  CLUS_1                            7                             18
  CLUS_2                            5                             15
  CLUS_3                            5                             19
D62V2, multiclass
        clus
vv       DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            7                             17
  CLUS_3                            6                             20
D62V3, multiclass
D62V4, multiclass
        clus
vv       DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE
  CLUS_1                            5                             21
  CLUS_2                           11                             27
  CLUS_3                            0                             29
D62V5, multiclass
        clus
vv       DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE
  CLUS_1                            6                             27
  CLUS_2                            7                             33
  CLUS_3                           13                             40
D62V6, multiclass
D62V7, multiclass
D62V8, multiclass
        clus
vv       DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE
  CLUS_1                            4                             15
  CLUS_2                            3                              9
  CLUS_3                            4                             15
D62V9, multiclass
D62V10, multiclass
        clus
vv       DEL PEAK 37(XP22.33) MUTATED DEL PEAK 37(XP22.33) WILD-TYPE
  CLUS_1                            3                             16
  CLUS_2                           14                             49
  CLUS_3                           14                             45
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"             "RPPA_CNMF"    "RPPA_CHIERARCHICAL" 
                     V7                      V8                      V9 
         "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF" 
                    V10 
 "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
