
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.4.4139/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.4.4139/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/411561/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LGG-TP/3144354/1.GDAC_mergedClustering.Finished/LGG-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LGG-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oT=LGG-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=222, in cluster file=220, common to both=220
[1]  43 220
[1] "Amp Peak  1(1q32.1)"
[1] 3
      AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE 
                           23                           197 
      AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE 
                           23                           197 
[1] "Amp Peak  2(4q12)"
[1] 3
      AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE 
                         10                         210 
      AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE 
                         10                         210 
[1] "Amp Peak  3(7p11.2)"
[1] 3
      AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE 
                           55                           165 
      AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE 
                           55                           165 
[1] "Amp Peak  4(7q32.3)"
[1] 3
      AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE 
                           77                           143 
      AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE 
                           77                           143 
[1] "Amp Peak  5(8q24.21)"
[1] 3
      AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE 
                            44                            176 
      AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE 
                            44                            176 
[1] "Amp Peak  6(10p15.1)"
[1] 3
      AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE 
                            35                            185 
      AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE 
                            35                            185 
[1] "Amp Peak  7(10q11.21)"
[1] 3
      AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE 
                              5                             215 
      AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE 
                              5                             215 
[1] "Amp Peak  8(11q23.3)"
[1] 3
      AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE 
                            38                            182 
      AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE 
                            38                            182 
[1] "Amp Peak  9(12p13.32)"
[1] 3
      AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE 
                             34                             186 
      AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE 
                             34                             186 
[1] "Amp Peak 10(12p11.22)"
[1] 3
      AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE 
                             21                             199 
      AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE 
                             21                             199 
[1] "Amp Peak 11(12q14.1)"
[1] 3
      AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE 
                            14                            206 
      AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE 
                            14                            206 
[1] "Amp Peak 12(19p13.3)"
[1] 3
      AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE 
                            51                            169 
      AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE 
                            51                            169 
[1] "Amp Peak 13(19q13.2)"
[1] 3
      AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE 
                            15                            205 
      AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE 
                            15                            205 
[1] "Amp Peak 14(Xp22.33)"
[1] 3
      AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE 
                            15                            205 
      AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE 
                            15                            205 
[1] "Amp Peak 15(Xq11.2)"
[1] 3
      AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE 
                           31                           189 
      AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE 
                           31                           189 
[1] "Del Peak  1(1p36.31)"
[1] 3
      DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE 
                            83                            137 
      DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE 
                            83                            137 
[1] "Del Peak  2(1p32.3)"
[1] 3
      DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE 
                           77                           143 
      DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE 
                           77                           143 
[1] "Del Peak  3(1q43)"
[1] 3
      DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE 
                         13                         207 
      DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE 
                         13                         207 
[1] "Del Peak  4(2q37.3)"
[1] 3
      DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE 
                           32                           188 
      DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE 
                           32                           188 
[1] "Del Peak  5(3p21.1)"
[1] 3
      DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE 
                           20                           200 
      DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE 
                           20                           200 
[1] "Del Peak  6(3q29)"
[1] 3
      DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE 
                         21                         199 
      DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE 
                         21                         199 
[1] "Del Peak  7(4q33)"
[1] 3
      DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE 
                         61                         159 
      DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE 
                         61                         159 
[1] "Del Peak  8(4q35.2)"
[1] 3
      DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE 
                           62                           158 
      DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE 
                           62                           158 
[1] "Del Peak  9(5q35.2)"
[1] 3
      DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE 
                           28                           192 
      DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE 
                           28                           192 
[1] "Del Peak 10(6p24.1)"
[1] 3
      DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE 
                           21                           199 
      DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE 
                           21                           199 
[1] "Del Peak 11(6q24.3)"
[1] 3
      DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE 
                           33                           187 
      DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE 
                           33                           187 
[1] "Del Peak 12(8p23.2)"
[1] 3
      DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE 
                           11                           209 
      DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE 
                           11                           209 
[1] "Del Peak 13(9p21.3)"
[1] 3
      DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE 
                           78                           142 
      DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE 
                           78                           142 
[1] "Del Peak 14(10q26.2)"
[1] 3
      DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE 
                            70                            150 
      DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE 
                            70                            150 
[1] "Del Peak 15(11p15.5)"
[1] 3
      DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE 
                            48                            172 
      DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE 
                            48                            172 
[1] "Del Peak 16(11q25)"
[1] 3
      DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE 
                          15                          205 
      DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE 
                          15                          205 
[1] "Del Peak 17(12q24.11)"
[1] 3
      DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE 
                             30                             190 
      DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE 
                             30                             190 
[1] "Del Peak 18(13q14.2)"
[1] 3
      DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE 
                            65                            155 
      DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE 
                            65                            155 
[1] "Del Peak 19(13q34)"
[1] 3
      DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE 
                          50                          170 
      DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE 
                          50                          170 
[1] "Del Peak 20(14q24.3)"
[1] 3
      DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE 
                            51                            169 
      DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE 
                            51                            169 
[1] "Del Peak 21(15q21.3)"
[1] 3
      DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE 
                            27                            193 
      DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE 
                            27                            193 
[1] "Del Peak 22(17q25.3)"
[1] 3
      DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE 
                            15                            205 
      DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE 
                            15                            205 
[1] "Del Peak 23(18p11.32)"
[1] 3
      DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE 
                             32                             188 
      DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE 
                             32                             188 
[1] "Del Peak 24(18q23)"
[1] 3
      DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE 
                          35                          185 
      DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE 
                          35                          185 
[1] "Del Peak 25(19q13.42)"
[1] 3
      DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE 
                            116                             104 
      DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE 
                            116                             104 
[1] "Del Peak 26(22q13.31)"
[1] 3
      DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE 
                             31                             189 
      DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE 
                             31                             189 
[1] "Del Peak 27(Xp22.31)"
[1] 3
      DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE 
                            51                            169 
      DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE 
                            51                            169 
[1] "Del Peak 28(Xq21.1)"
[1] 3
      DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE 
                           30                           190 
      DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE 
                           30                           190 
[1] "data2feature, selection=ALL"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 220 columns.

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

Clustering(1) Variable = Amp Peak  1(1q32.1)
D1V1, multiclass
[1] "Remove cluster labels:"  "AMP PEAK  1(1Q32.1) CNV"
clus
      AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE 
                            2                            25 
                   TCGA-CS-4942                    TCGA-CS-4943 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5396 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5270                    TCGA-DB-5273 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5274                    TCGA-DB-5275 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5276                    TCGA-DB-5278 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5280                    TCGA-DB-5281 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5140                    TCGA-DH-5141 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5142                    TCGA-DH-5143 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5144                    TCGA-E1-5302 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5303                    TCGA-E1-5304 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5311                    TCGA-E1-5318 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5322 
"AMP PEAK  1(1Q32.1) WILD-TYPE" 
D1V2, multiclass
[1] "Remove cluster labels:"  "AMP PEAK  1(1Q32.1) CNV"
clus
      AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE 
                            2                            25 
                   TCGA-CS-4942                    TCGA-CS-4943 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5396 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5270                    TCGA-DB-5273 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5274                    TCGA-DB-5275 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5276                    TCGA-DB-5278 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5280                    TCGA-DB-5281 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5140                    TCGA-DH-5141 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5142                    TCGA-DH-5143 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5144                    TCGA-E1-5302 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5303                    TCGA-E1-5304 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5311                    TCGA-E1-5318 
"AMP PEAK  1(1Q32.1) WILD-TYPE" "AMP PEAK  1(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5322 
"AMP PEAK  1(1Q32.1) WILD-TYPE" 
D1V3, multiclass
        clus
vv       AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE
  CLUS_1                       5                            89
  CLUS_2                      16                            34
  CLUS_3                       2                            74
D1V4, multiclass
        clus
vv       AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE
  CLUS_1                       8                            92
  CLUS_2                      12                            22
  CLUS_3                       2                            56
  CLUS_4                       1                            22
D1V5, multiclass
D1V6, multiclass
        clus
vv       AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE
  CLUS_1                       1                            31
  CLUS_2                      14                           103
  CLUS_3                       8                            61
D1V7, multiclass
        clus
vv       AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE
  CLUS_1                       6                            52
  CLUS_2                       2                            30
  CLUS_3                      11                            71
  CLUS_4                       4                            43
D1V8, multiclass
        clus
vv       AMP PEAK  1(1Q32.1) CNV AMP PEAK  1(1Q32.1) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      12                            83
  CLUS_3                       9                           107

Clustering(2) Variable = Amp Peak  2(4q12)
D2V1, multiclass
[1] "Remove cluster labels:" "AMP PEAK  2(4Q12) CNV" 
clus
      AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4944 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-CS-5390                  TCGA-CS-5394 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-CS-5395                  TCGA-CS-5396 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5270                  TCGA-DB-5273 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5274                  TCGA-DB-5275 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5276                  TCGA-DB-5278 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5302 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-E1-5303                  TCGA-E1-5304 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-E1-5311                  TCGA-E1-5318 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-E1-5322 
"AMP PEAK  2(4Q12) WILD-TYPE" 
D2V2, multiclass
[1] "Remove cluster labels:" "AMP PEAK  2(4Q12) CNV" 
clus
      AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4944 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-CS-5390                  TCGA-CS-5394 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-CS-5395                  TCGA-CS-5396 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5270                  TCGA-DB-5273 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5274                  TCGA-DB-5275 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5276                  TCGA-DB-5278 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5302 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-E1-5303                  TCGA-E1-5304 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-E1-5311                  TCGA-E1-5318 
"AMP PEAK  2(4Q12) WILD-TYPE" "AMP PEAK  2(4Q12) WILD-TYPE" 
                 TCGA-E1-5322 
"AMP PEAK  2(4Q12) WILD-TYPE" 
D2V3, multiclass
        clus
vv       AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE
  CLUS_1                     6                          88
  CLUS_2                     2                          48
  CLUS_3                     2                          74
D2V4, multiclass
        clus
vv       AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE
  CLUS_1                     7                          93
  CLUS_2                     1                          33
  CLUS_3                     1                          57
  CLUS_4                     1                          22
D2V5, multiclass
D2V6, multiclass
        clus
vv       AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE
  CLUS_1                     0                          32
  CLUS_2                     6                         111
  CLUS_3                     4                          65
D2V7, multiclass
        clus
vv       AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE
  CLUS_1                     1                          57
  CLUS_2                     2                          30
  CLUS_3                     5                          77
  CLUS_4                     2                          45
D2V8, multiclass
        clus
vv       AMP PEAK  2(4Q12) CNV AMP PEAK  2(4Q12) WILD-TYPE
  CLUS_1                     1                           7
  CLUS_2                     6                          89
  CLUS_3                     3                         113

Clustering(3) Variable = Amp Peak  3(7p11.2)
D3V1, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       2                             8
  CLUS_3                       2                             6
D3V2, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       2                             5
  CLUS_3                       2                             9
D3V3, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                       9                            85
  CLUS_2                      38                            12
  CLUS_3                       8                            68
D3V4, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                      17                            83
  CLUS_2                      27                             7
  CLUS_3                       6                            52
  CLUS_4                       3                            20
D3V5, multiclass
D3V6, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                       4                            28
  CLUS_2                      38                            79
  CLUS_3                      12                            57
D3V7, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                      19                            39
  CLUS_2                       3                            29
  CLUS_3                      12                            70
  CLUS_4                      20                            27
D3V8, multiclass
        clus
vv       AMP PEAK  3(7P11.2) CNV AMP PEAK  3(7P11.2) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      14                            81
  CLUS_3                      38                            78

Clustering(4) Variable = Amp Peak  4(7q32.3)
D4V1, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       2                             8
  CLUS_3                       3                             5
D4V2, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       3                             4
  CLUS_3                       2                             9
D4V3, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                      20                            74
  CLUS_2                      43                             7
  CLUS_3                      14                            62
D4V4, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                      35                            65
  CLUS_2                      25                             9
  CLUS_3                      12                            46
  CLUS_4                       3                            20
D4V5, multiclass
D4V6, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                       7                            25
  CLUS_2                      50                            67
  CLUS_3                      19                            50
D4V7, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                      24                            34
  CLUS_2                       7                            25
  CLUS_3                      22                            60
  CLUS_4                      23                            24
D4V8, multiclass
        clus
vv       AMP PEAK  4(7Q32.3) CNV AMP PEAK  4(7Q32.3) WILD-TYPE
  CLUS_1                       3                             5
  CLUS_2                      26                            69
  CLUS_3                      47                            69

Clustering(5) Variable = Amp Peak  5(8q24.21)
D5V1, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        1                              9
  CLUS_3                        3                              5
D5V2, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        2                              5
  CLUS_3                        2                              9
D5V3, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                       32                             62
  CLUS_2                        8                             42
  CLUS_3                        4                             72
D5V4, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                       36                             64
  CLUS_2                        4                             30
  CLUS_3                        3                             55
  CLUS_4                        1                             22
D5V5, multiclass
D5V6, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                        1                             31
  CLUS_2                       33                             84
  CLUS_3                       10                             59
D5V7, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                       17                             41
  CLUS_2                        4                             28
  CLUS_3                       11                             71
  CLUS_4                       12                             35
D5V8, multiclass
        clus
vv       AMP PEAK  5(8Q24.21) CNV AMP PEAK  5(8Q24.21) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       13                             82
  CLUS_3                       31                             85

Clustering(6) Variable = Amp Peak  6(10p15.1)
D6V1, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                        3                              6
  CLUS_2                        1                              9
  CLUS_3                        1                              7
D6V2, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                        3                              6
  CLUS_2                        1                              6
  CLUS_3                        1                             10
D6V3, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                       31                             63
  CLUS_2                        3                             47
  CLUS_3                        1                             75
D6V4, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                       31                             69
  CLUS_2                        2                             32
  CLUS_3                        0                             58
  CLUS_4                        2                             21
D6V5, multiclass
D6V6, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                        0                             32
  CLUS_2                       25                             92
  CLUS_3                       10                             59
D6V7, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                        9                             49
  CLUS_2                        2                             30
  CLUS_3                       11                             71
  CLUS_4                       13                             34
D6V8, multiclass
        clus
vv       AMP PEAK  6(10P15.1) CNV AMP PEAK  6(10P15.1) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       14                             81
  CLUS_3                       21                             95

Clustering(7) Variable = Amp Peak  7(10q11.21)
D7V1, multiclass
[1] "Remove cluster labels:"    "AMP PEAK  7(10Q11.21) CNV"
clus
      AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE 
                              2                              25 
                     TCGA-CS-4942                      TCGA-CS-4943 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-CS-4944                      TCGA-CS-5390 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-CS-5394                      TCGA-CS-5395 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-CS-5396                      TCGA-DB-5270 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5273                      TCGA-DB-5274 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5275                      TCGA-DB-5276 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5278                      TCGA-DB-5280 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5281                      TCGA-DH-5140 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DH-5141                      TCGA-DH-5142 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DH-5143                      TCGA-DH-5144 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-E1-5302                      TCGA-E1-5303 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-E1-5311                      TCGA-E1-5318 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-E1-5322 
"AMP PEAK  7(10Q11.21) WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:"    "AMP PEAK  7(10Q11.21) CNV"
clus
      AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE 
                              2                              25 
                     TCGA-CS-4942                      TCGA-CS-4943 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-CS-4944                      TCGA-CS-5390 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-CS-5394                      TCGA-CS-5395 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-CS-5396                      TCGA-DB-5270 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5273                      TCGA-DB-5274 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5275                      TCGA-DB-5276 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5278                      TCGA-DB-5280 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DB-5281                      TCGA-DH-5140 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DH-5141                      TCGA-DH-5142 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-DH-5143                      TCGA-DH-5144 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-E1-5302                      TCGA-E1-5303 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-E1-5311                      TCGA-E1-5318 
"AMP PEAK  7(10Q11.21) WILD-TYPE" "AMP PEAK  7(10Q11.21) WILD-TYPE" 
                     TCGA-E1-5322 
"AMP PEAK  7(10Q11.21) WILD-TYPE" 
D7V3, multiclass
        clus
vv       AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE
  CLUS_1                         4                              90
  CLUS_2                         1                              49
  CLUS_3                         0                              76
D7V4, multiclass
        clus
vv       AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE
  CLUS_1                         4                              96
  CLUS_2                         1                              33
  CLUS_3                         0                              58
  CLUS_4                         0                              23
D7V5, multiclass
D7V6, multiclass
        clus
vv       AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE
  CLUS_1                         0                              32
  CLUS_2                         5                             112
  CLUS_3                         0                              69
D7V7, multiclass
        clus
vv       AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE
  CLUS_1                         0                              58
  CLUS_2                         1                              31
  CLUS_3                         0                              82
  CLUS_4                         4                              43
D7V8, multiclass
        clus
vv       AMP PEAK  7(10Q11.21) CNV AMP PEAK  7(10Q11.21) WILD-TYPE
  CLUS_1                         0                               8
  CLUS_2                         2                              93
  CLUS_3                         3                             113

Clustering(8) Variable = Amp Peak  8(11q23.3)
D8V1, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        4                              6
  CLUS_3                        1                              7
D8V2, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        0                              7
  CLUS_3                        5                              6
D8V3, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                       17                             77
  CLUS_2                        9                             41
  CLUS_3                       12                             64
D8V4, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                       24                             76
  CLUS_2                        2                             32
  CLUS_3                       10                             48
  CLUS_4                        1                             22
D8V5, multiclass
D8V6, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                        9                             23
  CLUS_2                       19                             98
  CLUS_3                       10                             59
D8V7, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                       10                             48
  CLUS_2                        8                             24
  CLUS_3                       12                             70
  CLUS_4                        8                             39
D8V8, multiclass
        clus
vv       AMP PEAK  8(11Q23.3) CNV AMP PEAK  8(11Q23.3) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       16                             79
  CLUS_3                       22                             94

Clustering(9) Variable = Amp Peak  9(12p13.32)
D9V1, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                         3                               6
  CLUS_2                         2                               8
  CLUS_3                         2                               6
D9V2, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                         3                               6
  CLUS_2                         1                               6
  CLUS_3                         3                               8
D9V3, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                        27                              67
  CLUS_2                         4                              46
  CLUS_3                         3                              73
D9V4, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                        28                              72
  CLUS_2                         3                              31
  CLUS_3                         2                              56
  CLUS_4                         1                              22
D9V5, multiclass
D9V6, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                         2                              30
  CLUS_2                        28                              89
  CLUS_3                         4                              65
D9V7, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                         8                              50
  CLUS_2                         5                              27
  CLUS_3                         7                              75
  CLUS_4                        14                              33
D9V8, multiclass
        clus
vv       AMP PEAK  9(12P13.32) CNV AMP PEAK  9(12P13.32) WILD-TYPE
  CLUS_1                         0                               8
  CLUS_2                         9                              86
  CLUS_3                        25                              91

Clustering(10) Variable = Amp Peak 10(12p11.22)
D10V1, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                         2                               7
  CLUS_2                         2                               8
  CLUS_3                         1                               7
D10V2, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                         2                               7
  CLUS_2                         0                               7
  CLUS_3                         3                               8
D10V3, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                        15                              79
  CLUS_2                         3                              47
  CLUS_3                         3                              73
D10V4, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                        16                              84
  CLUS_2                         2                              32
  CLUS_3                         2                              56
  CLUS_4                         1                              22
D10V5, multiclass
D10V6, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                         2                              30
  CLUS_2                        18                              99
  CLUS_3                         1                              68
D10V7, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                         4                              54
  CLUS_2                         4                              28
  CLUS_3                         4                              78
  CLUS_4                         9                              38
D10V8, multiclass
        clus
vv       AMP PEAK 10(12P11.22) CNV AMP PEAK 10(12P11.22) WILD-TYPE
  CLUS_1                         0                               8
  CLUS_2                         5                              90
  CLUS_3                        16                             100

Clustering(11) Variable = Amp Peak 11(12q14.1)
D11V1, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 11(12Q14.1) CNV"
clus
      AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5277                     TCGA-DB-5278 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5280                     TCGA-DB-5281 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5140                     TCGA-DH-5141 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5142                     TCGA-DH-5143 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5144                     TCGA-E1-5302 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5322 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
D11V2, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 11(12Q14.1) CNV"
clus
      AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5277                     TCGA-DB-5278 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5280                     TCGA-DB-5281 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5140                     TCGA-DH-5141 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5142                     TCGA-DH-5143 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5144                     TCGA-E1-5302 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5322 
"AMP PEAK 11(12Q14.1) WILD-TYPE" "AMP PEAK 11(12Q14.1) WILD-TYPE" 
D11V3, multiclass
        clus
vv       AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE
  CLUS_1                        3                             91
  CLUS_2                        6                             44
  CLUS_3                        5                             71
D11V4, multiclass
        clus
vv       AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE
  CLUS_1                        7                             93
  CLUS_2                        4                             30
  CLUS_3                        3                             55
  CLUS_4                        0                             23
D11V5, multiclass
D11V6, multiclass
        clus
vv       AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE
  CLUS_1                        3                             29
  CLUS_2                        9                            108
  CLUS_3                        2                             67
D11V7, multiclass
        clus
vv       AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE
  CLUS_1                        4                             54
  CLUS_2                        1                             31
  CLUS_3                        6                             76
  CLUS_4                        3                             44
D11V8, multiclass
        clus
vv       AMP PEAK 11(12Q14.1) CNV AMP PEAK 11(12Q14.1) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                        5                             90
  CLUS_3                        8                            108

Clustering(12) Variable = Amp Peak 12(19p13.3)
D12V1, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        5                              5
  CLUS_3                        2                              6
D12V2, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        2                              5
  CLUS_3                        5                              6
D12V3, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                        4                             90
  CLUS_2                       15                             35
  CLUS_3                       32                             44
D12V4, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                       10                             90
  CLUS_2                       10                             24
  CLUS_3                       25                             33
  CLUS_4                        2                             21
D12V5, multiclass
D12V6, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                       15                             17
  CLUS_2                       20                             97
  CLUS_3                       15                             54
D12V7, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                        9                             49
  CLUS_2                       10                             22
  CLUS_3                       21                             61
  CLUS_4                       11                             36
D12V8, multiclass
        clus
vv       AMP PEAK 12(19P13.3) CNV AMP PEAK 12(19P13.3) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       26                             69
  CLUS_3                       23                             93

Clustering(13) Variable = Amp Peak 13(19q13.2)
D13V1, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        0                             10
  CLUS_3                        1                              7
D13V2, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        1                              6
  CLUS_3                        0                             11
D13V3, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        1                             93
  CLUS_2                       12                             38
  CLUS_3                        2                             74
D13V4, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        5                             95
  CLUS_2                        8                             26
  CLUS_3                        0                             58
  CLUS_4                        1                             22
D13V5, multiclass
D13V6, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        0                             32
  CLUS_2                       13                            104
  CLUS_3                        1                             68
D13V7, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        7                             51
  CLUS_2                        0                             32
  CLUS_3                        2                             80
  CLUS_4                        6                             41
D13V8, multiclass
        clus
vv       AMP PEAK 13(19Q13.2) CNV AMP PEAK 13(19Q13.2) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                        1                             94
  CLUS_3                       13                            103

Clustering(14) Variable = Amp Peak 14(Xp22.33)
D14V1, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 14(XP22.33) CNV"
clus
      AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE 
                             2                             25 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5318 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-E1-5322 
"AMP PEAK 14(XP22.33) WILD-TYPE" 
D14V2, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 14(XP22.33) CNV"
clus
      AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE 
                             2                             25 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5318 
"AMP PEAK 14(XP22.33) WILD-TYPE" "AMP PEAK 14(XP22.33) WILD-TYPE" 
                    TCGA-E1-5322 
"AMP PEAK 14(XP22.33) WILD-TYPE" 
D14V3, multiclass
        clus
vv       AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE
  CLUS_1                       11                             83
  CLUS_2                        4                             46
  CLUS_3                        0                             76
D14V4, multiclass
        clus
vv       AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE
  CLUS_1                       12                             88
  CLUS_2                        3                             31
  CLUS_3                        0                             58
  CLUS_4                        0                             23
D14V5, multiclass
D14V6, multiclass
        clus
vv       AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE
  CLUS_1                        0                             32
  CLUS_2                       12                            105
  CLUS_3                        3                             66
D14V7, multiclass
        clus
vv       AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE
  CLUS_1                        3                             55
  CLUS_2                        1                             31
  CLUS_3                        5                             77
  CLUS_4                        6                             41
D14V8, multiclass
        clus
vv       AMP PEAK 14(XP22.33) CNV AMP PEAK 14(XP22.33) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                        7                             88
  CLUS_3                        7                            109

Clustering(15) Variable = Amp Peak 15(Xq11.2)
D15V1, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       0                            10
  CLUS_3                       2                             6
D15V2, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       1                             6
  CLUS_3                       1                            10
D15V3, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                      26                            68
  CLUS_2                       2                            48
  CLUS_3                       3                            73
D15V4, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                      27                            73
  CLUS_2                       3                            31
  CLUS_3                       0                            58
  CLUS_4                       1                            22
D15V5, multiclass
D15V6, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                       0                            32
  CLUS_2                      26                            91
  CLUS_3                       5                            64
D15V7, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                      10                            48
  CLUS_2                       2                            30
  CLUS_3                       8                            74
  CLUS_4                      11                            36
D15V8, multiclass
        clus
vv       AMP PEAK 15(XQ11.2) CNV AMP PEAK 15(XQ11.2) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      11                            84
  CLUS_3                      20                            96

Clustering(16) Variable = Del Peak  1(1p36.31)
D16V1, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        8                              2
  CLUS_3                        2                              6
D16V2, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        2                              5
  CLUS_3                        8                              3
D16V3, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        7                             87
  CLUS_2                        9                             41
  CLUS_3                       67                              9
D16V4, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        6                             94
  CLUS_2                        8                             26
  CLUS_3                       58                              0
  CLUS_4                        7                             16
D16V5, multiclass
D16V6, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                       32                              0
  CLUS_2                       19                             98
  CLUS_3                       32                             37
D16V7, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                       12                             46
  CLUS_2                       22                             10
  CLUS_3                       41                             41
  CLUS_4                        8                             39
D16V8, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        3                              5
  CLUS_2                       48                             47
  CLUS_3                       32                             84

Clustering(17) Variable = Del Peak  2(1p32.3)
D17V1, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       7                             3
  CLUS_3                       2                             6
D17V2, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             5
  CLUS_3                       7                             4
D17V3, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       5                            89
  CLUS_2                       4                            46
  CLUS_3                      68                             8
D17V4, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       4                            96
  CLUS_2                       5                            29
  CLUS_3                      58                             0
  CLUS_4                       7                            16
D17V5, multiclass
D17V6, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                      32                             0
  CLUS_2                      13                           104
  CLUS_3                      32                            37
D17V7, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                      11                            47
  CLUS_2                      22                            10
  CLUS_3                      41                            41
  CLUS_4                       3                            44
D17V8, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       3                             5
  CLUS_2                      48                            47
  CLUS_3                      26                            90

Clustering(18) Variable = Del Peak  3(1q43)
D18V1, multiclass
[1] "Remove cluster labels:" "DEL PEAK  3(1Q43) CNV" 
clus
      DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4943 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-CS-4944                  TCGA-CS-5390 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-CS-5394                  TCGA-CS-5395 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-CS-5396                  TCGA-DB-5270 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5273                  TCGA-DB-5274 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5275                  TCGA-DB-5276 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5277                  TCGA-DB-5278 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5303 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-E1-5304                  TCGA-E1-5311 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-E1-5318 
"DEL PEAK  3(1Q43) WILD-TYPE" 
D18V2, multiclass
[1] "Remove cluster labels:" "DEL PEAK  3(1Q43) CNV" 
clus
      DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4943 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-CS-4944                  TCGA-CS-5390 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-CS-5394                  TCGA-CS-5395 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-CS-5396                  TCGA-DB-5270 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5273                  TCGA-DB-5274 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5275                  TCGA-DB-5276 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5277                  TCGA-DB-5278 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5303 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-E1-5304                  TCGA-E1-5311 
"DEL PEAK  3(1Q43) WILD-TYPE" "DEL PEAK  3(1Q43) WILD-TYPE" 
                 TCGA-E1-5318 
"DEL PEAK  3(1Q43) WILD-TYPE" 
D18V3, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     7                          87
  CLUS_2                     3                          47
  CLUS_3                     3                          73
D18V4, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     8                          92
  CLUS_2                     3                          31
  CLUS_3                     1                          57
  CLUS_4                     1                          22
D18V5, multiclass
D18V6, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     0                          32
  CLUS_2                    11                         106
  CLUS_3                     2                          67
D18V7, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     4                          54
  CLUS_2                     2                          30
  CLUS_3                     3                          79
  CLUS_4                     4                          43
D18V8, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     0                           8
  CLUS_2                     3                          92
  CLUS_3                    10                         106

Clustering(19) Variable = Del Peak  4(2q37.3)
D19V1, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       1                             9
  CLUS_3                       4                             4
D19V2, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       3                             4
  CLUS_3                       2                             9
D19V3, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                      21                            73
  CLUS_2                       8                            42
  CLUS_3                       3                            73
D19V4, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                      28                            72
  CLUS_2                       1                            33
  CLUS_3                       2                            56
  CLUS_4                       1                            22
D19V5, multiclass
D19V6, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                       1                            31
  CLUS_2                      24                            93
  CLUS_3                       7                            62
D19V7, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                      11                            47
  CLUS_2                       5                            27
  CLUS_3                       6                            76
  CLUS_4                      10                            37
D19V8, multiclass
        clus
vv       DEL PEAK  4(2Q37.3) CNV DEL PEAK  4(2Q37.3) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      10                            85
  CLUS_3                      22                            94

Clustering(20) Variable = Del Peak  5(3p21.1)
D20V1, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             8
  CLUS_3                       1                             7
D20V2, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       0                             7
  CLUS_3                       3                             8
D20V3, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                      11                            83
  CLUS_2                       5                            45
  CLUS_3                       4                            72
D20V4, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                      15                            85
  CLUS_2                       2                            32
  CLUS_3                       2                            56
  CLUS_4                       0                            23
D20V5, multiclass
D20V6, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                       1                            31
  CLUS_2                      17                           100
  CLUS_3                       2                            67
D20V7, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                       7                            51
  CLUS_2                       4                            28
  CLUS_3                       2                            80
  CLUS_4                       7                            40
D20V8, multiclass
        clus
vv       DEL PEAK  5(3P21.1) CNV DEL PEAK  5(3P21.1) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                       3                            92
  CLUS_3                      16                           100

Clustering(21) Variable = Del Peak  6(3q29)
D21V1, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                     1                           8
  CLUS_2                     0                          10
  CLUS_3                     2                           6
D21V2, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                     1                           8
  CLUS_2                     1                           6
  CLUS_3                     1                          10
D21V3, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                    15                          79
  CLUS_2                     4                          46
  CLUS_3                     2                          74
D21V4, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                    18                          82
  CLUS_2                     1                          33
  CLUS_3                     1                          57
  CLUS_4                     1                          22
D21V5, multiclass
D21V6, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                     0                          32
  CLUS_2                    15                         102
  CLUS_3                     6                          63
D21V7, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                     7                          51
  CLUS_2                     1                          31
  CLUS_3                     7                          75
  CLUS_4                     6                          41
D21V8, multiclass
        clus
vv       DEL PEAK  6(3Q29) CNV DEL PEAK  6(3Q29) WILD-TYPE
  CLUS_1                     2                           6
  CLUS_2                     7                          88
  CLUS_3                    12                         104

Clustering(22) Variable = Del Peak  7(4q33)
D22V1, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                     4                           5
  CLUS_2                     4                           6
  CLUS_3                     3                           5
D22V2, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                     4                           5
  CLUS_2                     2                           5
  CLUS_3                     5                           6
D22V3, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                    25                          69
  CLUS_2                     5                          45
  CLUS_3                    31                          45
D22V4, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                    31                          69
  CLUS_2                     3                          31
  CLUS_3                    25                          33
  CLUS_4                     2                          21
D22V5, multiclass
D22V6, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                    15                          17
  CLUS_2                    25                          92
  CLUS_3                    20                          49
D22V7, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                     7                          51
  CLUS_2                    17                          15
  CLUS_3                    24                          58
  CLUS_4                    13                          34
D22V8, multiclass
        clus
vv       DEL PEAK  7(4Q33) CNV DEL PEAK  7(4Q33) WILD-TYPE
  CLUS_1                     2                           6
  CLUS_2                    32                          63
  CLUS_3                    27                          89

Clustering(23) Variable = Del Peak  8(4q35.2)
D23V1, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       4                             5
  CLUS_2                       4                             6
  CLUS_3                       3                             5
D23V2, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       4                             5
  CLUS_2                       2                             5
  CLUS_3                       5                             6
D23V3, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      26                            68
  CLUS_2                       4                            46
  CLUS_3                      32                            44
D23V4, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      33                            67
  CLUS_2                       2                            32
  CLUS_3                      25                            33
  CLUS_4                       2                            21
D23V5, multiclass
D23V6, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      15                            17
  CLUS_2                      25                            92
  CLUS_3                      21                            48
D23V7, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       8                            50
  CLUS_2                      17                            15
  CLUS_3                      25                            57
  CLUS_4                      12                            35
D23V8, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      33                            62
  CLUS_3                      27                            89

Clustering(24) Variable = Del Peak  9(5q35.2)
D24V1, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             8
  CLUS_3                       3                             5
D24V2, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             5
  CLUS_3                       3                             8
D24V3, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                      20                            74
  CLUS_2                       5                            45
  CLUS_3                       3                            73
D24V4, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                      20                            80
  CLUS_2                       5                            29
  CLUS_3                       0                            58
  CLUS_4                       3                            20
D24V5, multiclass
D24V6, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       0                            32
  CLUS_2                      22                            95
  CLUS_3                       6                            63
D24V7, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       4                            54
  CLUS_2                       2                            30
  CLUS_3                       9                            73
  CLUS_4                      13                            34
D24V8, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       3                             5
  CLUS_2                      10                            85
  CLUS_3                      15                           101

Clustering(25) Variable = Del Peak 10(6p24.1)
D25V1, multiclass
[1] "Remove cluster labels:"  "DEL PEAK 10(6P24.1) CNV"
clus
      DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE 
                            2                            25 
                   TCGA-CS-4942                    TCGA-CS-4943 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5395 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-CS-5396                    TCGA-DB-5270 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5273                    TCGA-DB-5274 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5275                    TCGA-DB-5276 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5278                    TCGA-DB-5280 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5281                    TCGA-DH-5140 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DH-5141                    TCGA-DH-5142 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DH-5143                    TCGA-DH-5144 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-E1-5302                    TCGA-E1-5303 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-E1-5311                    TCGA-E1-5318 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-E1-5322 
"DEL PEAK 10(6P24.1) WILD-TYPE" 
D25V2, multiclass
[1] "Remove cluster labels:"  "DEL PEAK 10(6P24.1) CNV"
clus
      DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE 
                            2                            25 
                   TCGA-CS-4942                    TCGA-CS-4943 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5395 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-CS-5396                    TCGA-DB-5270 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5273                    TCGA-DB-5274 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5275                    TCGA-DB-5276 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5278                    TCGA-DB-5280 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DB-5281                    TCGA-DH-5140 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DH-5141                    TCGA-DH-5142 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-DH-5143                    TCGA-DH-5144 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-E1-5302                    TCGA-E1-5303 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-E1-5311                    TCGA-E1-5318 
"DEL PEAK 10(6P24.1) WILD-TYPE" "DEL PEAK 10(6P24.1) WILD-TYPE" 
                   TCGA-E1-5322 
"DEL PEAK 10(6P24.1) WILD-TYPE" 
D25V3, multiclass
        clus
vv       DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE
  CLUS_1                       9                            85
  CLUS_2                       8                            42
  CLUS_3                       4                            72
D25V4, multiclass
        clus
vv       DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE
  CLUS_1                      11                            89
  CLUS_2                       5                            29
  CLUS_3                       3                            55
  CLUS_4                       1                            22
D25V5, multiclass
D25V6, multiclass
        clus
vv       DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE
  CLUS_1                       3                            29
  CLUS_2                      14                           103
  CLUS_3                       3                            66
D25V7, multiclass
        clus
vv       DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE
  CLUS_1                       5                            53
  CLUS_2                       3                            29
  CLUS_3                       6                            76
  CLUS_4                       7                            40
D25V8, multiclass
        clus
vv       DEL PEAK 10(6P24.1) CNV DEL PEAK 10(6P24.1) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                       7                            88
  CLUS_3                      13                           103

Clustering(26) Variable = Del Peak 11(6q24.3)
D26V1, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       0                            10
  CLUS_3                       0                             8
D26V2, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       0                             7
  CLUS_3                       0                            11
D26V3, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                      12                            82
  CLUS_2                      14                            36
  CLUS_3                       7                            69
D26V4, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                      22                            78
  CLUS_2                       8                            26
  CLUS_3                       2                            56
  CLUS_4                       1                            22
D26V5, multiclass
D26V6, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       2                            30
  CLUS_2                      24                            93
  CLUS_3                       7                            62
D26V7, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                      16                            42
  CLUS_2                       4                            28
  CLUS_3                       9                            73
  CLUS_4                       4                            43
D26V8, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                      10                            85
  CLUS_3                      22                            94

Clustering(27) Variable = Del Peak 12(8p23.2)
D27V1, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       2                             8
  CLUS_3                       1                             7
D27V2, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       0                             7
  CLUS_3                       3                             8
D27V3, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       3                            91
  CLUS_2                       7                            43
  CLUS_3                       1                            75
D27V4, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       6                            94
  CLUS_2                       5                            29
  CLUS_3                       0                            58
  CLUS_4                       0                            23
D27V5, multiclass
D27V6, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       0                            32
  CLUS_2                       8                           109
  CLUS_3                       3                            66
D27V7, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       2                            56
  CLUS_2                       3                            29
  CLUS_3                       2                            80
  CLUS_4                       4                            43
D27V8, multiclass
        clus
vv       DEL PEAK 12(8P23.2) CNV DEL PEAK 12(8P23.2) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                       3                            92
  CLUS_3                       8                           108

Clustering(28) Variable = Del Peak 13(9p21.3)
D28V1, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       4                             6
  CLUS_3                       3                             5
D28V2, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             5
  CLUS_3                       5                             6
D28V3, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                      28                            66
  CLUS_2                      34                            16
  CLUS_3                      16                            60
D28V4, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                      38                            62
  CLUS_2                      23                            11
  CLUS_3                      12                            46
  CLUS_4                       3                            20
D28V5, multiclass
D28V6, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                       9                            23
  CLUS_2                      50                            67
  CLUS_3                      18                            51
D28V7, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                      22                            36
  CLUS_2                      13                            19
  CLUS_3                      24                            58
  CLUS_4                      19                            28
D28V8, multiclass
        clus
vv       DEL PEAK 13(9P21.3) CNV DEL PEAK 13(9P21.3) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      28                            67
  CLUS_3                      48                            68

Clustering(29) Variable = Del Peak 14(10q26.2)
D29V1, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        2                              8
  CLUS_3                        3                              5
D29V2, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        2                              5
  CLUS_3                        3                              8
D29V3, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                       27                             67
  CLUS_2                       39                             11
  CLUS_3                        4                             72
D29V4, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                       33                             67
  CLUS_2                       30                              4
  CLUS_3                        3                             55
  CLUS_4                        3                             20
D29V5, multiclass
D29V6, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                        1                             31
  CLUS_2                       55                             62
  CLUS_3                       12                             57
D29V7, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                       23                             35
  CLUS_2                        6                             26
  CLUS_3                       13                             69
  CLUS_4                       28                             19
D29V8, multiclass
        clus
vv       DEL PEAK 14(10Q26.2) CNV DEL PEAK 14(10Q26.2) WILD-TYPE
  CLUS_1                        3                              5
  CLUS_2                       18                             77
  CLUS_3                       49                             67

Clustering(30) Variable = Del Peak 15(11p15.5)
D30V1, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                        3                              6
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D30V2, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                        3                              6
  CLUS_2                        0                              7
  CLUS_3                        4                              7
D30V3, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                       35                             59
  CLUS_2                       10                             40
  CLUS_3                        3                             73
D30V4, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                       40                             60
  CLUS_2                        5                             29
  CLUS_3                        0                             58
  CLUS_4                        3                             20
D30V5, multiclass
D30V6, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                        0                             32
  CLUS_2                       34                             83
  CLUS_3                       13                             56
D30V7, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                       10                             48
  CLUS_2                        7                             25
  CLUS_3                       15                             67
  CLUS_4                       16                             31
D30V8, multiclass
        clus
vv       DEL PEAK 15(11P15.5) CNV DEL PEAK 15(11P15.5) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                       18                             77
  CLUS_3                       29                             87

Clustering(31) Variable = Del Peak 16(11q25)
D31V1, multiclass
[1] "Remove cluster labels:" "DEL PEAK 16(11Q25) CNV"
clus
      DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE 
                           1                           26 
                  TCGA-CS-4942                   TCGA-CS-4943 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-CS-4944                   TCGA-CS-5390 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-CS-5394                   TCGA-CS-5395 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-CS-5396                   TCGA-DB-5270 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5273                   TCGA-DB-5274 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5275                   TCGA-DB-5276 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5277                   TCGA-DB-5278 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5280                   TCGA-DB-5281 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DH-5141                   TCGA-DH-5142 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DH-5143                   TCGA-DH-5144 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-E1-5302                   TCGA-E1-5303 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-E1-5304                   TCGA-E1-5311 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-E1-5318                   TCGA-E1-5322 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
D31V2, multiclass
[1] "Remove cluster labels:" "DEL PEAK 16(11Q25) CNV"
clus
      DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE 
                           1                           26 
                  TCGA-CS-4942                   TCGA-CS-4943 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-CS-4944                   TCGA-CS-5390 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-CS-5394                   TCGA-CS-5395 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-CS-5396                   TCGA-DB-5270 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5273                   TCGA-DB-5274 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5275                   TCGA-DB-5276 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5277                   TCGA-DB-5278 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DB-5280                   TCGA-DB-5281 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DH-5141                   TCGA-DH-5142 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-DH-5143                   TCGA-DH-5144 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-E1-5302                   TCGA-E1-5303 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-E1-5304                   TCGA-E1-5311 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
                  TCGA-E1-5318                   TCGA-E1-5322 
"DEL PEAK 16(11Q25) WILD-TYPE" "DEL PEAK 16(11Q25) WILD-TYPE" 
D31V3, multiclass
        clus
vv       DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE
  CLUS_1                      8                           86
  CLUS_2                      7                           43
  CLUS_3                      0                           76
D31V4, multiclass
        clus
vv       DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE
  CLUS_1                      9                           91
  CLUS_2                      5                           29
  CLUS_3                      0                           58
  CLUS_4                      1                           22
D31V5, multiclass
D31V6, multiclass
        clus
vv       DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE
  CLUS_1                      0                           32
  CLUS_2                     12                          105
  CLUS_3                      3                           66
D31V7, multiclass
        clus
vv       DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE
  CLUS_1                      4                           54
  CLUS_2                      2                           30
  CLUS_3                      3                           79
  CLUS_4                      6                           41
D31V8, multiclass
        clus
vv       DEL PEAK 16(11Q25) CNV DEL PEAK 16(11Q25) WILD-TYPE
  CLUS_1                      1                            7
  CLUS_2                      3                           92
  CLUS_3                     11                          105

Clustering(32) Variable = Del Peak 17(12q24.11)
D32V1, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                         2                               7
  CLUS_2                         2                               8
  CLUS_3                         1                               7
D32V2, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                         2                               7
  CLUS_2                         0                               7
  CLUS_3                         3                               8
D32V3, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                        24                              70
  CLUS_2                         3                              47
  CLUS_3                         3                              73
D32V4, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                        26                              74
  CLUS_2                         1                              33
  CLUS_3                         1                              57
  CLUS_4                         2                              21
D32V5, multiclass
D32V6, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                         0                              32
  CLUS_2                        22                              95
  CLUS_3                         8                              61
D32V7, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                         3                              55
  CLUS_2                         4                              28
  CLUS_3                        11                              71
  CLUS_4                        12                              35
D32V8, multiclass
        clus
vv       DEL PEAK 17(12Q24.11) CNV DEL PEAK 17(12Q24.11) WILD-TYPE
  CLUS_1                         0                               8
  CLUS_2                        12                              83
  CLUS_3                        18                              98

Clustering(33) Variable = Del Peak 18(13q14.2)
D33V1, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                        5                              4
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D33V2, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                        5                              4
  CLUS_2                        0                              7
  CLUS_3                        4                              7
D33V3, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                       31                             63
  CLUS_2                       19                             31
  CLUS_3                       15                             61
D33V4, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                       36                             64
  CLUS_2                       15                             19
  CLUS_3                       11                             47
  CLUS_4                        3                             20
D33V5, multiclass
D33V6, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                        6                             26
  CLUS_2                       40                             77
  CLUS_3                       18                             51
D33V7, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                       15                             43
  CLUS_2                       10                             22
  CLUS_3                       21                             61
  CLUS_4                       19                             28
D33V8, multiclass
        clus
vv       DEL PEAK 18(13Q14.2) CNV DEL PEAK 18(13Q14.2) WILD-TYPE
  CLUS_1                        3                              5
  CLUS_2                       26                             69
  CLUS_3                       36                             80

Clustering(34) Variable = Del Peak 19(13q34)
D34V1, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                      2                            7
  CLUS_2                      2                            8
  CLUS_3                      0                            8
D34V2, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                      2                            7
  CLUS_2                      0                            7
  CLUS_3                      2                            9
D34V3, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                     22                           72
  CLUS_2                     15                           35
  CLUS_3                     13                           63
D34V4, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                     24                           76
  CLUS_2                     13                           21
  CLUS_3                     10                           48
  CLUS_4                      3                           20
D34V5, multiclass
D34V6, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                      5                           27
  CLUS_2                     33                           84
  CLUS_3                     12                           57
D34V7, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                     10                           48
  CLUS_2                      7                           25
  CLUS_3                     15                           67
  CLUS_4                     18                           29
D34V8, multiclass
        clus
vv       DEL PEAK 19(13Q34) CNV DEL PEAK 19(13Q34) WILD-TYPE
  CLUS_1                      2                            6
  CLUS_2                     18                           77
  CLUS_3                     30                           86

Clustering(35) Variable = Del Peak 20(14q24.3)
D35V1, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                        4                              5
  CLUS_2                        2                              8
  CLUS_3                        1                              7
D35V2, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                        4                              5
  CLUS_2                        1                              6
  CLUS_3                        2                              9
D35V3, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                       18                             76
  CLUS_2                       21                             29
  CLUS_3                       12                             64
D35V4, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                       27                             73
  CLUS_2                       13                             21
  CLUS_3                        7                             51
  CLUS_4                        3                             20
D35V5, multiclass
D35V6, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                        5                             27
  CLUS_2                       34                             83
  CLUS_3                       12                             57
D35V7, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                       23                             35
  CLUS_2                        4                             28
  CLUS_3                       15                             67
  CLUS_4                        9                             38
D35V8, multiclass
        clus
vv       DEL PEAK 20(14Q24.3) CNV DEL PEAK 20(14Q24.3) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       14                             81
  CLUS_3                       35                             81

Clustering(36) Variable = Del Peak 21(15q21.3)
D36V1, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        2                              8
  CLUS_3                        2                              6
D36V2, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        2                              5
  CLUS_3                        2                              9
D36V3, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                        6                             88
  CLUS_2                        8                             42
  CLUS_3                       13                             63
D36V4, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                       10                             90
  CLUS_2                        6                             28
  CLUS_3                       11                             47
  CLUS_4                        0                             23
D36V5, multiclass
D36V6, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                        7                             25
  CLUS_2                       13                            104
  CLUS_3                        7                             62
D36V7, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                        9                             49
  CLUS_2                        5                             27
  CLUS_3                       10                             72
  CLUS_4                        3                             44
D36V8, multiclass
        clus
vv       DEL PEAK 21(15Q21.3) CNV DEL PEAK 21(15Q21.3) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       10                             85
  CLUS_3                       15                            101

Clustering(37) Variable = Del Peak 22(17q25.3)
D37V1, multiclass
[1] "Remove cluster labels:"   "DEL PEAK 22(17Q25.3) CNV"
clus
      DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5276                     TCGA-DB-5277 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-E1-5302                     TCGA-E1-5303 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-E1-5304                     TCGA-E1-5311 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-E1-5318                     TCGA-E1-5322 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
D37V2, multiclass
[1] "Remove cluster labels:"   "DEL PEAK 22(17Q25.3) CNV"
clus
      DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5276                     TCGA-DB-5277 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-E1-5302                     TCGA-E1-5303 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-E1-5304                     TCGA-E1-5311 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
                    TCGA-E1-5318                     TCGA-E1-5322 
"DEL PEAK 22(17Q25.3) WILD-TYPE" "DEL PEAK 22(17Q25.3) WILD-TYPE" 
D37V3, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                       11                             83
  CLUS_2                        3                             47
  CLUS_3                        1                             75
D37V4, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        9                             91
  CLUS_2                        4                             30
  CLUS_3                        1                             57
  CLUS_4                        1                             22
D37V5, multiclass
D37V6, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        1                             31
  CLUS_2                       11                            106
  CLUS_3                        3                             66
D37V7, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        6                             52
  CLUS_2                        1                             31
  CLUS_3                        3                             79
  CLUS_4                        5                             42
D37V8, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                        5                             90
  CLUS_3                       10                            106

Clustering(38) Variable = Del Peak 23(18p11.32)
D38V1, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         2                               7
  CLUS_2                         3                               7
  CLUS_3                         0                               8
D38V2, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         2                               7
  CLUS_2                         0                               7
  CLUS_3                         3                               8
D38V3, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                        16                              78
  CLUS_2                         5                              45
  CLUS_3                        11                              65
D38V4, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                        18                              82
  CLUS_2                         5                              29
  CLUS_3                         9                              49
  CLUS_4                         0                              23
D38V5, multiclass
D38V6, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         5                              27
  CLUS_2                        15                             102
  CLUS_3                        12                              57
D38V7, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         6                              52
  CLUS_2                         6                              26
  CLUS_3                        12                              70
  CLUS_4                         8                              39
D38V8, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         0                               8
  CLUS_2                        13                              82
  CLUS_3                        19                              97

Clustering(39) Variable = Del Peak 24(18q23)
D39V1, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      2                            7
  CLUS_2                      3                            7
  CLUS_3                      0                            8
D39V2, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      2                            7
  CLUS_2                      0                            7
  CLUS_3                      3                            8
D39V3, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                     15                           79
  CLUS_2                      7                           43
  CLUS_3                     13                           63
D39V4, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                     18                           82
  CLUS_2                      6                           28
  CLUS_3                     11                           47
  CLUS_4                      0                           23
D39V5, multiclass
D39V6, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      6                           26
  CLUS_2                     18                           99
  CLUS_3                     11                           58
D39V7, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      9                           49
  CLUS_2                      7                           25
  CLUS_3                     11                           71
  CLUS_4                      8                           39
D39V8, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      1                            7
  CLUS_2                     11                           84
  CLUS_3                     23                           93

Clustering(40) Variable = Del Peak 25(19q13.42)
D40V1, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         7                               2
  CLUS_2                        10                               0
  CLUS_3                         4                               4
D40V2, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         7                               2
  CLUS_2                         3                               4
  CLUS_3                        11                               0
D40V3, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        26                              68
  CLUS_2                        14                              36
  CLUS_3                        76                               0
D40V4, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        44                              56
  CLUS_2                         4                              30
  CLUS_3                        58                               0
  CLUS_4                         7                              16
D40V5, multiclass
D40V6, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        32                               0
  CLUS_2                        42                              75
  CLUS_3                        42                              27
D40V7, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        25                              33
  CLUS_2                        28                               4
  CLUS_3                        50                              32
  CLUS_4                        13                              34
D40V8, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         4                               4
  CLUS_2                        59                              36
  CLUS_3                        53                              63

Clustering(41) Variable = Del Peak 26(22q13.31)
D41V1, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         4                               5
  CLUS_2                         1                               9
  CLUS_3                         1                               7
D41V2, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         4                               5
  CLUS_2                         0                               7
  CLUS_3                         2                               9
D41V3, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                        14                              80
  CLUS_2                        16                              34
  CLUS_3                         1                              75
D41V4, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                        19                              81
  CLUS_2                        10                              24
  CLUS_3                         0                              58
  CLUS_4                         1                              22
D41V5, multiclass
D41V6, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         0                              32
  CLUS_2                        24                              93
  CLUS_3                         6                              63
D41V7, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         8                              50
  CLUS_2                         4                              28
  CLUS_3                         8                              74
  CLUS_4                        11                              36
D41V8, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         1                               7
  CLUS_2                         9                              86
  CLUS_3                        21                              95

Clustering(42) Variable = Del Peak 27(Xp22.31)
D42V1, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        3                              7
  CLUS_3                        2                              6
D42V2, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        2                              5
  CLUS_3                        3                              8
D42V3, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                       25                             69
  CLUS_2                        9                             41
  CLUS_3                       17                             59
D42V4, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                       29                             71
  CLUS_2                        7                             27
  CLUS_3                       13                             45
  CLUS_4                        2                             21
D42V5, multiclass
D42V6, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                       10                             22
  CLUS_2                       30                             87
  CLUS_3                       10                             59
D42V7, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                       14                             44
  CLUS_2                       12                             20
  CLUS_3                       11                             71
  CLUS_4                       14                             33
D42V8, multiclass
        clus
vv       DEL PEAK 27(XP22.31) CNV DEL PEAK 27(XP22.31) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                       17                             78
  CLUS_3                       33                             83

Clustering(43) Variable = Del Peak 28(Xq21.1)
D43V1, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       3                             7
  CLUS_3                       2                             6
D43V2, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       1                             6
  CLUS_3                       4                             7
D43V3, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                      10                            84
  CLUS_2                       7                            43
  CLUS_3                      13                            63
D43V4, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                      12                            88
  CLUS_2                       6                            28
  CLUS_3                      12                            46
  CLUS_4                       0                            23
D43V5, multiclass
D43V6, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       9                            23
  CLUS_2                      16                           101
  CLUS_3                       5                            64
D43V7, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       4                            54
  CLUS_2                      12                            20
  CLUS_3                       4                            78
  CLUS_4                      10                            37
D43V8, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                      12                            83
  CLUS_3                      17                            99
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
