
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/477045/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LGG-TP/4431190/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=296, in cluster file=269, common to both=269
[1]  48 269
[1] "Amp Peak  1(1q22)"
[1] 3
      AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE 
                         27                         242 
      AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE 
                         27                         242 
[1] "Amp Peak  2(1q32.1)"
[1] 3
      AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE 
                           27                           242 
      AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE 
                           27                           242 
[1] "Amp Peak  3(3p24.3)"
[1] 3
      AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE 
                           14                           255 
      AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE 
                           14                           255 
[1] "Amp Peak  4(3q26.32)"
[1] 3
      AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE 
                            14                            255 
      AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE 
                            14                            255 
[1] "Amp Peak  5(4q12)"
[1] 3
      AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE 
                         14                         255 
      AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE 
                         14                         255 
[1] "Amp Peak  6(7p11.2)"
[1] 3
      AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE 
                           73                           196 
      AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE 
                           73                           196 
[1] "Amp Peak  7(7q32.3)"
[1] 3
      AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE 
                          100                           169 
      AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE 
                          100                           169 
[1] "Amp Peak  8(8q24.12)"
[1] 3
      AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE 
                            55                            214 
      AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE 
                            55                            214 
[1] "Amp Peak  9(10p15.3)"
[1] 3
      AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE 
                            41                            228 
      AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE 
                            41                            228 
[1] "Amp Peak 10(11q23.3)"
[1] 3
      AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE 
                            45                            224 
      AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE 
                            45                            224 
[1] "Amp Peak 11(12p13.32)"
[1] 3
      AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE 
                             43                             226 
      AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE 
                             43                             226 
[1] "Amp Peak 12(12p12.1)"
[1] 3
      AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE 
                            28                            241 
      AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE 
                            28                            241 
[1] "Amp Peak 13(12q14.1)"
[1] 3
      AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE 
                            19                            250 
      AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE 
                            19                            250 
[1] "Amp Peak 14(13q33.3)"
[1] 3
      AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE 
                            15                            254 
      AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE 
                            15                            254 
[1] "Amp Peak 15(17q25.1)"
[1] 3
      AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE 
                            16                            253 
      AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE 
                            16                            253 
[1] "Amp Peak 16(18q23)"
[1] 3
      AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE 
                          12                          257 
      AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE 
                          12                          257 
[1] "Amp Peak 17(19p13.3)"
[1] 3
      AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE 
                            60                            209 
      AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE 
                            60                            209 
[1] "Amp Peak 18(19q13.2)"
[1] 3
      AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE 
                            19                            250 
      AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE 
                            19                            250 
[1] "Amp Peak 19(Xp22.33)"
[1] 3
      AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE 
                            18                            251 
      AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE 
                            18                            251 
[1] "Amp Peak 20(Xp11.22)"
[1] 3
      AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE 
                            38                            231 
      AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE 
                            38                            231 
[1] "Del Peak  1(1p36.31)"
[1] 3
      DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE 
                            96                            173 
      DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE 
                            96                            173 
[1] "Del Peak  2(1p32.3)"
[1] 3
      DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE 
                           88                           181 
      DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE 
                           88                           181 
[1] "Del Peak  3(1q43)"
[1] 3
      DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE 
                         15                         254 
      DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE 
                         15                         254 
[1] "Del Peak  4(2p25.3)"
[1] 3
      DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE 
                           24                           245 
      DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE 
                           24                           245 
[1] "Del Peak  5(2q37.1)"
[1] 3
      DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE 
                           33                           236 
      DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE 
                           33                           236 
[1] "Del Peak  6(2q37.3)"
[1] 3
      DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE 
                           40                           229 
      DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE 
                           40                           229 
[1] "Del Peak  7(3p21.1)"
[1] 3
      DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE 
                           28                           241 
      DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE 
                           28                           241 
[1] "Del Peak  8(4q35.2)"
[1] 3
      DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE 
                           76                           193 
      DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE 
                           76                           193 
[1] "Del Peak  9(5q35.2)"
[1] 3
      DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE 
                           34                           235 
      DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE 
                           34                           235 
[1] "Del Peak 10(6p25.3)"
[1] 3
      DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE 
                           28                           241 
      DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE 
                           28                           241 
[1] "Del Peak 11(6q24.3)"
[1] 3
      DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE 
                           45                           224 
      DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE 
                           45                           224 
[1] "Del Peak 12(9p21.3)"
[1] 3
      DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE 
                           99                           170 
      DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE 
                           99                           170 
[1] "Del Peak 13(10q26.3)"
[1] 3
      DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE 
                            81                            188 
      DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE 
                            81                            188 
[1] "Del Peak 14(11p15.5)"
[1] 3
      DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE 
                            57                            212 
      DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE 
                            57                            212 
[1] "Del Peak 15(11q25)"
[1] 3
      DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE 
                          21                          248 
      DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE 
                          21                          248 
[1] "Del Peak 16(12q12)"
[1] 3
      DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE 
                          35                          234 
      DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE 
                          35                          234 
[1] "Del Peak 17(13q14.2)"
[1] 3
      DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE 
                            77                            192 
      DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE 
                            77                            192 
[1] "Del Peak 18(13q21.2)"
[1] 3
      DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE 
                            80                            189 
      DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE 
                            80                            189 
[1] "Del Peak 19(13q22.1)"
[1] 3
      DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE 
                            77                            192 
      DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE 
                            77                            192 
[1] "Del Peak 20(13q34)"
[1] 3
      DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE 
                          57                          212 
      DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE 
                          57                          212 
[1] "Del Peak 21(14q24.3)"
[1] 3
      DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE 
                            61                            208 
      DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE 
                            61                            208 
[1] "Del Peak 22(17q25.3)"
[1] 3
      DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE 
                            17                            252 
      DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE 
                            17                            252 
[1] "Del Peak 23(18p11.32)"
[1] 3
      DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE 
                             42                             227 
      DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE 
                             42                             227 
[1] "Del Peak 24(18q23)"
[1] 3
      DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE 
                          43                          226 
      DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE 
                          43                          226 
[1] "Del Peak 25(19q13.42)"
[1] 3
      DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE 
                            136                             133 
      DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE 
                            136                             133 
[1] "Del Peak 26(22q13.31)"
[1] 3
      DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE 
                             40                             229 
      DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE 
                             40                             229 
[1] "Del Peak 27(Xp22.2)"
[1] 3
      DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE 
                           58                           211 
      DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE 
                           58                           211 
[1] "Del Peak 28(Xq21.1)"
[1] 3
      DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE 
                           35                           234 
      DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE 
                           35                           234 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 269 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 269 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=8, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1q22)
D1V1, multiclass
[1] "Remove cluster labels:" "AMP PEAK  1(1Q22) CNV" 
clus
      AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4943 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-CS-4944                  TCGA-CS-5390 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-CS-5394                  TCGA-CS-5395 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-CS-5396                  TCGA-DB-5270 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5273                  TCGA-DB-5274 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5275                  TCGA-DB-5276 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5277                  TCGA-DB-5278 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5303 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-E1-5311                  TCGA-E1-5318 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-E1-5322 
"AMP PEAK  1(1Q22) WILD-TYPE" 
D1V2, multiclass
[1] "Remove cluster labels:" "AMP PEAK  1(1Q22) CNV" 
clus
      AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4943 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-CS-4944                  TCGA-CS-5390 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-CS-5394                  TCGA-CS-5395 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-CS-5396                  TCGA-DB-5270 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5273                  TCGA-DB-5274 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5275                  TCGA-DB-5276 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5277                  TCGA-DB-5278 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5303 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-E1-5311                  TCGA-E1-5318 
"AMP PEAK  1(1Q22) WILD-TYPE" "AMP PEAK  1(1Q22) WILD-TYPE" 
                 TCGA-E1-5322 
"AMP PEAK  1(1Q22) WILD-TYPE" 
D1V3, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                     5                          47
  CLUS_2                     9                          48
  CLUS_3                    11                          43
  CLUS_4                     2                         104
D1V4, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                    15                         107
  CLUS_2                     7                          35
  CLUS_3                     4                          62
  CLUS_4                     1                          33
D1V5, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                     4                          48
  CLUS_2                    10                          52
  CLUS_3                     4                          64
  CLUS_4                     6                          68
D1V6, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                     0                           8
  CLUS_2                    15                         114
  CLUS_3                     9                         110
D1V7, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                    14                          80
  CLUS_2                     6                          72
  CLUS_3                     7                          90
D1V8, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                     3                          33
  CLUS_2                    18                         123
  CLUS_3                     6                          86
D1V9, multiclass
D1V10, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                     3                          11
  CLUS_2                    14                         131
  CLUS_3                    10                          99
D1V11, multiclass
D1V12, multiclass
        clus
vv       AMP PEAK  1(1Q22) CNV AMP PEAK  1(1Q22) WILD-TYPE
  CLUS_1                     6                          36
  CLUS_2                    11                          94
  CLUS_3                    10                         111

Clustering(2) Variable = Amp Peak  2(1q32.1)
D2V1, multiclass
[1] "Remove cluster labels:"  "AMP PEAK  2(1Q32.1) CNV"
clus
      AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE 
                            2                            25 
                   TCGA-CS-4942                    TCGA-CS-4943 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5396 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5270                    TCGA-DB-5273 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5274                    TCGA-DB-5275 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5276                    TCGA-DB-5278 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5280                    TCGA-DB-5281 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5140                    TCGA-DH-5141 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5142                    TCGA-DH-5143 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5144                    TCGA-E1-5302 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5303                    TCGA-E1-5304 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5311                    TCGA-E1-5318 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5322 
"AMP PEAK  2(1Q32.1) WILD-TYPE" 
D2V2, multiclass
[1] "Remove cluster labels:"  "AMP PEAK  2(1Q32.1) CNV"
clus
      AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE 
                            2                            25 
                   TCGA-CS-4942                    TCGA-CS-4943 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5396 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5270                    TCGA-DB-5273 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5274                    TCGA-DB-5275 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5276                    TCGA-DB-5278 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DB-5280                    TCGA-DB-5281 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5140                    TCGA-DH-5141 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5142                    TCGA-DH-5143 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-DH-5144                    TCGA-E1-5302 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5303                    TCGA-E1-5304 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5311                    TCGA-E1-5318 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-E1-5322 
"AMP PEAK  2(1Q32.1) WILD-TYPE" 
D2V3, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                       2                            50
  CLUS_2                      15                            42
  CLUS_3                       9                            45
  CLUS_4                       1                           105
D2V4, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                       9                           113
  CLUS_2                      15                            27
  CLUS_3                       2                            64
  CLUS_4                       1                            33
D2V5, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                       4                            48
  CLUS_2                       9                            53
  CLUS_3                       2                            66
  CLUS_4                       8                            66
D2V6, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      13                           116
  CLUS_3                      10                           109
D2V7, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                      15                            79
  CLUS_2                       2                            76
  CLUS_3                      10                            87
D2V8, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                       1                            35
  CLUS_2                      17                           124
  CLUS_3                       9                            83
D2V9, multiclass
D2V10, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                       7                             7
  CLUS_2                       9                           136
  CLUS_3                      11                            98
D2V11, multiclass
D2V12, multiclass
        clus
vv       AMP PEAK  2(1Q32.1) CNV AMP PEAK  2(1Q32.1) WILD-TYPE
  CLUS_1                      13                            29
  CLUS_2                       4                           101
  CLUS_3                      10                           111

Clustering(3) Variable = Amp Peak  3(3p24.3)
D3V1, multiclass
[1] "Remove cluster labels:"  "AMP PEAK  3(3P24.3) CNV"
clus
      AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE 
                            1                            26 
                   TCGA-CS-4942                    TCGA-CS-4943 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5395 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-CS-5396                    TCGA-DB-5270 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5273                    TCGA-DB-5274 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5275                    TCGA-DB-5276 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5278                    TCGA-DB-5280 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5281                    TCGA-DH-5140 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DH-5141                    TCGA-DH-5142 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DH-5143                    TCGA-DH-5144 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-E1-5302                    TCGA-E1-5303 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-E1-5304                    TCGA-E1-5311 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-E1-5318                    TCGA-E1-5322 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
D3V2, multiclass
[1] "Remove cluster labels:"  "AMP PEAK  3(3P24.3) CNV"
clus
      AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE 
                            1                            26 
                   TCGA-CS-4942                    TCGA-CS-4943 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5395 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-CS-5396                    TCGA-DB-5270 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5273                    TCGA-DB-5274 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5275                    TCGA-DB-5276 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5278                    TCGA-DB-5280 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DB-5281                    TCGA-DH-5140 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DH-5141                    TCGA-DH-5142 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-DH-5143                    TCGA-DH-5144 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-E1-5302                    TCGA-E1-5303 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-E1-5304                    TCGA-E1-5311 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
                   TCGA-E1-5318                    TCGA-E1-5322 
"AMP PEAK  3(3P24.3) WILD-TYPE" "AMP PEAK  3(3P24.3) WILD-TYPE" 
D3V3, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       2                            50
  CLUS_2                       3                            54
  CLUS_3                       7                            47
  CLUS_4                       2                           104
D3V4, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       8                           114
  CLUS_2                       2                            40
  CLUS_3                       3                            63
  CLUS_4                       1                            33
D3V5, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       3                            49
  CLUS_2                       4                            58
  CLUS_3                       3                            65
  CLUS_4                       3                            71
D3V6, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                      10                           119
  CLUS_3                       2                           117
D3V7, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       9                            85
  CLUS_2                       2                            76
  CLUS_3                       3                            94
D3V8, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       2                            34
  CLUS_2                      10                           131
  CLUS_3                       2                            90
D3V9, multiclass
D3V10, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       1                            13
  CLUS_2                       8                           137
  CLUS_3                       5                           104
D3V11, multiclass
D3V12, multiclass
        clus
vv       AMP PEAK  3(3P24.3) CNV AMP PEAK  3(3P24.3) WILD-TYPE
  CLUS_1                       3                            39
  CLUS_2                       6                            99
  CLUS_3                       5                           116

Clustering(4) Variable = Amp Peak  4(3q26.32)
D4V1, multiclass
[1] "Remove cluster labels:"   "AMP PEAK  4(3Q26.32) CNV"
clus
      AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE 
                             2                             25 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5396 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5270                     TCGA-DB-5273 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5274                     TCGA-DB-5275 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5276                     TCGA-DB-5277 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-E1-5302                     TCGA-E1-5303 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5318 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-E1-5322 
"AMP PEAK  4(3Q26.32) WILD-TYPE" 
D4V2, multiclass
[1] "Remove cluster labels:"   "AMP PEAK  4(3Q26.32) CNV"
clus
      AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE 
                             2                             25 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5396 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5270                     TCGA-DB-5273 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5274                     TCGA-DB-5275 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5276                     TCGA-DB-5277 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-E1-5302                     TCGA-E1-5303 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5318 
"AMP PEAK  4(3Q26.32) WILD-TYPE" "AMP PEAK  4(3Q26.32) WILD-TYPE" 
                    TCGA-E1-5322 
"AMP PEAK  4(3Q26.32) WILD-TYPE" 
D4V3, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        2                             50
  CLUS_2                        6                             51
  CLUS_3                        6                             48
  CLUS_4                        0                            106
D4V4, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        7                            115
  CLUS_2                        5                             37
  CLUS_3                        2                             64
  CLUS_4                        0                             34
D4V5, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        0                             52
  CLUS_2                        7                             55
  CLUS_3                        1                             67
  CLUS_4                        3                             71
D4V6, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                        7                            122
  CLUS_3                        4                            115
D4V7, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        7                             87
  CLUS_2                        3                             75
  CLUS_3                        4                             93
D4V8, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        1                             35
  CLUS_2                       10                            131
  CLUS_3                        3                             89
D4V9, multiclass
D4V10, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        1                             13
  CLUS_2                        8                            137
  CLUS_3                        5                            104
D4V11, multiclass
D4V12, multiclass
        clus
vv       AMP PEAK  4(3Q26.32) CNV AMP PEAK  4(3Q26.32) WILD-TYPE
  CLUS_1                        4                             38
  CLUS_2                        6                             99
  CLUS_3                        4                            117

Clustering(5) Variable = Amp Peak  5(4q12)
D5V1, multiclass
[1] "Remove cluster labels:" "AMP PEAK  5(4Q12) CNV" 
clus
      AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4944 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-CS-5390                  TCGA-CS-5394 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-CS-5395                  TCGA-CS-5396 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5270                  TCGA-DB-5273 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5274                  TCGA-DB-5275 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5276                  TCGA-DB-5278 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5302 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-E1-5303                  TCGA-E1-5304 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-E1-5311                  TCGA-E1-5318 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-E1-5322 
"AMP PEAK  5(4Q12) WILD-TYPE" 
D5V2, multiclass
[1] "Remove cluster labels:" "AMP PEAK  5(4Q12) CNV" 
clus
      AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE 
                          2                          25 
                 TCGA-CS-4942                  TCGA-CS-4944 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-CS-5390                  TCGA-CS-5394 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-CS-5395                  TCGA-CS-5396 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5270                  TCGA-DB-5273 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5274                  TCGA-DB-5275 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5276                  TCGA-DB-5278 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DB-5280                  TCGA-DB-5281 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DH-5140                  TCGA-DH-5141 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DH-5142                  TCGA-DH-5143 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-DH-5144                  TCGA-E1-5302 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-E1-5303                  TCGA-E1-5304 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-E1-5311                  TCGA-E1-5318 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-E1-5322 
"AMP PEAK  5(4Q12) WILD-TYPE" 
D5V3, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     1                          51
  CLUS_2                     2                          55
  CLUS_3                     9                          45
  CLUS_4                     2                         104
D5V4, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                    10                         112
  CLUS_2                     2                          40
  CLUS_3                     1                          65
  CLUS_4                     1                          33
D5V5, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     2                          50
  CLUS_2                     7                          55
  CLUS_3                     0                          68
  CLUS_4                     5                          69
D5V6, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     0                           8
  CLUS_2                     6                         123
  CLUS_3                     8                         111
D5V7, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     6                          88
  CLUS_2                     3                          75
  CLUS_3                     5                          92
D5V8, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     0                          36
  CLUS_2                     9                         132
  CLUS_3                     5                          87
D5V9, multiclass
D5V10, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     1                          13
  CLUS_2                     5                         140
  CLUS_3                     8                         101
D5V11, multiclass
D5V12, multiclass
        clus
vv       AMP PEAK  5(4Q12) CNV AMP PEAK  5(4Q12) WILD-TYPE
  CLUS_1                     3                          39
  CLUS_2                     4                         101
  CLUS_3                     7                         114

Clustering(6) Variable = Amp Peak  6(7p11.2)
D6V1, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       2                             8
  CLUS_3                       2                             6
D6V2, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                       1                             6
  CLUS_2                       1                             5
  CLUS_3                       4                             6
  CLUS_4                       1                             3
D6V3, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                       4                            48
  CLUS_2                      50                             7
  CLUS_3                      12                            42
  CLUS_4                       7                            99
D6V4, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                      22                           100
  CLUS_2                      35                             7
  CLUS_3                       8                            58
  CLUS_4                       6                            28
D6V5, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                      13                            39
  CLUS_2                      30                            32
  CLUS_3                      12                            56
  CLUS_4                      12                            62
D6V6, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      44                            85
  CLUS_3                      23                            96
D6V7, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                      42                            52
  CLUS_2                      15                            63
  CLUS_3                      16                            81
D6V8, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                       5                            31
  CLUS_2                      52                            89
  CLUS_3                      16                            76
D6V9, multiclass
D6V10, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                      11                             3
  CLUS_2                      43                           102
  CLUS_3                      18                            91
D6V11, multiclass
D6V12, multiclass
        clus
vv       AMP PEAK  6(7P11.2) CNV AMP PEAK  6(7P11.2) WILD-TYPE
  CLUS_1                      31                            11
  CLUS_2                      24                            81
  CLUS_3                      17                           104

Clustering(7) Variable = Amp Peak  7(7q32.3)
D7V1, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                       3                             6
  CLUS_2                       2                             8
  CLUS_3                       3                             5
D7V2, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                       1                             6
  CLUS_2                       2                             4
  CLUS_3                       4                             6
  CLUS_4                       1                             3
D7V3, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                      13                            39
  CLUS_2                      53                             4
  CLUS_3                      17                            37
  CLUS_4                      17                            89
D7V4, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                      45                            77
  CLUS_2                      32                            10
  CLUS_3                      15                            51
  CLUS_4                       6                            28
D7V5, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                      20                            32
  CLUS_2                      33                            29
  CLUS_3                      18                            50
  CLUS_4                      22                            52
D7V6, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      54                            75
  CLUS_3                      39                            80
D7V7, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                      50                            44
  CLUS_2                      25                            53
  CLUS_3                      25                            72
D7V8, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                       9                            27
  CLUS_2                      67                            74
  CLUS_3                      24                            68
D7V9, multiclass
D7V10, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                      10                             4
  CLUS_2                      58                            87
  CLUS_3                      31                            78
D7V11, multiclass
D7V12, multiclass
        clus
vv       AMP PEAK  7(7Q32.3) CNV AMP PEAK  7(7Q32.3) WILD-TYPE
  CLUS_1                      29                            13
  CLUS_2                      37                            68
  CLUS_3                      33                            88

Clustering(8) Variable = Amp Peak  8(8q24.12)
D8V1, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        1                              9
  CLUS_3                        3                              5
D8V2, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        2                              4
  CLUS_3                        2                              8
  CLUS_4                        2                              2
D8V3, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                       17                             35
  CLUS_2                       11                             46
  CLUS_3                       25                             29
  CLUS_4                        2                            104
D8V4, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                       46                             76
  CLUS_2                        4                             38
  CLUS_3                        3                             63
  CLUS_4                        2                             32
D8V5, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                       15                             37
  CLUS_2                       12                             50
  CLUS_3                       19                             49
  CLUS_4                        8                             66
D8V6, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       28                            101
  CLUS_3                       24                             95
D8V7, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                       18                             76
  CLUS_2                       21                             57
  CLUS_3                       16                             81
D8V8, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                        2                             34
  CLUS_2                       38                            103
  CLUS_3                       15                             77
D8V9, multiclass
D8V10, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                        2                             12
  CLUS_2                       36                            109
  CLUS_3                       17                             92
D8V11, multiclass
D8V12, multiclass
        clus
vv       AMP PEAK  8(8Q24.12) CNV AMP PEAK  8(8Q24.12) WILD-TYPE
  CLUS_1                        4                             38
  CLUS_2                       33                             72
  CLUS_3                       18                            103

Clustering(9) Variable = Amp Peak  9(10p15.3)
D9V1, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                        3                              6
  CLUS_2                        1                              9
  CLUS_3                        2                              6
D9V2, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        1                              5
  CLUS_3                        3                              7
  CLUS_4                        2                              2
D9V3, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                       19                             33
  CLUS_2                        5                             52
  CLUS_3                       15                             39
  CLUS_4                        2                            104
D9V4, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                       36                             86
  CLUS_2                        1                             41
  CLUS_3                        0                             66
  CLUS_4                        4                             30
D9V5, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                       13                             39
  CLUS_2                        9                             53
  CLUS_3                       12                             56
  CLUS_4                        5                             69
D9V6, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       23                            106
  CLUS_3                       14                            105
D9V7, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                       15                             79
  CLUS_2                       15                             63
  CLUS_3                       11                             86
D9V8, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                        0                             36
  CLUS_2                       31                            110
  CLUS_3                       10                             82
D9V9, multiclass
D9V10, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                        2                             12
  CLUS_2                       27                            118
  CLUS_3                       12                             97
D9V11, multiclass
D9V12, multiclass
        clus
vv       AMP PEAK  9(10P15.3) CNV AMP PEAK  9(10P15.3) WILD-TYPE
  CLUS_1                        3                             39
  CLUS_2                       23                             82
  CLUS_3                       15                            106

Clustering(10) Variable = Amp Peak 10(11q23.3)
D10V1, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D10V2, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        2                              5
  CLUS_2                        0                              6
  CLUS_3                        0                             10
  CLUS_4                        2                              2
D10V3, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                       14                             38
  CLUS_2                        8                             49
  CLUS_3                        9                             45
  CLUS_4                       14                             92
D10V4, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                       27                             95
  CLUS_2                        3                             39
  CLUS_3                       10                             56
  CLUS_4                        4                             30
D10V5, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        5                             47
  CLUS_2                        9                             53
  CLUS_3                       18                             50
  CLUS_4                       13                             61
D10V6, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       28                            101
  CLUS_3                       17                            102
D10V7, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                       14                             80
  CLUS_2                       16                             62
  CLUS_3                       15                             82
D10V8, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        8                             28
  CLUS_2                       22                            119
  CLUS_3                       15                             77
D10V9, multiclass
D10V10, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        3                             11
  CLUS_2                       26                            119
  CLUS_3                       16                             93
D10V11, multiclass
D10V12, multiclass
        clus
vv       AMP PEAK 10(11Q23.3) CNV AMP PEAK 10(11Q23.3) WILD-TYPE
  CLUS_1                        4                             38
  CLUS_2                       22                             83
  CLUS_3                       19                            102

Clustering(11) Variable = Amp Peak 11(12p13.32)
D11V1, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         3                               6
  CLUS_2                         2                               8
  CLUS_3                         2                               6
D11V2, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         0                               7
  CLUS_2                         1                               5
  CLUS_3                         3                               7
  CLUS_4                         3                               1
D11V3, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                        20                              32
  CLUS_2                         8                              49
  CLUS_3                        14                              40
  CLUS_4                         1                             105
D11V4, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                        33                              89
  CLUS_2                         5                              37
  CLUS_3                         2                              64
  CLUS_4                         3                              31
D11V5, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         9                              43
  CLUS_2                        16                              46
  CLUS_3                         9                              59
  CLUS_4                         8                              66
D11V6, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         2                               6
  CLUS_2                        25                             104
  CLUS_3                        15                             104
D11V7, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                        18                              76
  CLUS_2                        17                              61
  CLUS_3                         8                              89
D11V8, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         2                              34
  CLUS_2                        33                             108
  CLUS_3                         8                              84
D11V9, multiclass
D11V10, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         1                              13
  CLUS_2                        31                             114
  CLUS_3                        11                              98
D11V11, multiclass
D11V12, multiclass
        clus
vv       AMP PEAK 11(12P13.32) CNV AMP PEAK 11(12P13.32) WILD-TYPE
  CLUS_1                         7                              35
  CLUS_2                        23                              82
  CLUS_3                        13                             108

Clustering(12) Variable = Amp Peak 12(12p12.1)
D12V1, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        2                              8
  CLUS_3                        1                              7
D12V2, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        0                              6
  CLUS_3                        2                              8
  CLUS_4                        3                              1
D12V3, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                       12                             40
  CLUS_2                        5                             52
  CLUS_3                       10                             44
  CLUS_4                        1                            105
D12V4, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                       20                            102
  CLUS_2                        4                             38
  CLUS_3                        2                             64
  CLUS_4                        2                             32
D12V5, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        6                             46
  CLUS_2                       11                             51
  CLUS_3                        5                             63
  CLUS_4                        5                             69
D12V6, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                       15                            114
  CLUS_3                       11                            108
D12V7, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                       12                             82
  CLUS_2                       14                             64
  CLUS_3                        2                             95
D12V8, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        2                             34
  CLUS_2                       24                            117
  CLUS_3                        2                             90
D12V9, multiclass
D12V10, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        0                             14
  CLUS_2                       22                            123
  CLUS_3                        6                            103
D12V11, multiclass
D12V12, multiclass
        clus
vv       AMP PEAK 12(12P12.1) CNV AMP PEAK 12(12P12.1) WILD-TYPE
  CLUS_1                        6                             36
  CLUS_2                       14                             91
  CLUS_3                        8                            113

Clustering(13) Variable = Amp Peak 13(12q14.1)
D13V1, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 13(12Q14.1) CNV"
clus
      AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5277                     TCGA-DB-5278 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5280                     TCGA-DB-5281 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5140                     TCGA-DH-5141 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5142                     TCGA-DH-5143 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5144                     TCGA-E1-5302 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5322 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
D13V2, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 13(12Q14.1) CNV"
clus
      AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5277                     TCGA-DB-5278 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DB-5280                     TCGA-DB-5281 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5140                     TCGA-DH-5141 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5142                     TCGA-DH-5143 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-DH-5144                     TCGA-E1-5302 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5322 
"AMP PEAK 13(12Q14.1) WILD-TYPE" "AMP PEAK 13(12Q14.1) WILD-TYPE" 
D13V3, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        1                             51
  CLUS_2                        6                             51
  CLUS_3                       11                             43
  CLUS_4                        1                            105
D13V4, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        8                            114
  CLUS_2                        7                             35
  CLUS_3                        3                             63
  CLUS_4                        1                             33
D13V5, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        2                             50
  CLUS_2                        9                             53
  CLUS_3                        1                             67
  CLUS_4                        4                             70
D13V6, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                        9                            120
  CLUS_3                        7                            112
D13V7, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                       12                             82
  CLUS_2                        4                             74
  CLUS_3                        3                             94
D13V8, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        3                             33
  CLUS_2                       12                            129
  CLUS_3                        4                             88
D13V9, multiclass
D13V10, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        2                             12
  CLUS_2                       12                            133
  CLUS_3                        5                            104
D13V11, multiclass
D13V12, multiclass
        clus
vv       AMP PEAK 13(12Q14.1) CNV AMP PEAK 13(12Q14.1) WILD-TYPE
  CLUS_1                        8                             34
  CLUS_2                        5                            100
  CLUS_3                        6                            115

Clustering(14) Variable = Amp Peak 14(13q33.3)
D14V1, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 14(13Q33.3) CNV"
clus
      AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-E1-5302                     TCGA-E1-5303 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-E1-5304                     TCGA-E1-5311 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-E1-5318                     TCGA-E1-5322 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
D14V2, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 14(13Q33.3) CNV"
clus
      AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE 
                             1                             26 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-E1-5302                     TCGA-E1-5303 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-E1-5304                     TCGA-E1-5311 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
                    TCGA-E1-5318                     TCGA-E1-5322 
"AMP PEAK 14(13Q33.3) WILD-TYPE" "AMP PEAK 14(13Q33.3) WILD-TYPE" 
D14V3, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        5                             47
  CLUS_2                        3                             54
  CLUS_3                        7                             47
  CLUS_4                        0                            106
D14V4, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                       13                            109
  CLUS_2                        2                             40
  CLUS_3                        0                             66
  CLUS_4                        0                             34
D14V5, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        2                             50
  CLUS_2                        7                             55
  CLUS_3                        3                             65
  CLUS_4                        2                             72
D14V6, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       10                            119
  CLUS_3                        4                            115
D14V7, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        7                             87
  CLUS_2                        5                             73
  CLUS_3                        3                             94
D14V8, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        0                             36
  CLUS_2                       12                            129
  CLUS_3                        3                             89
D14V9, multiclass
D14V10, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        0                             14
  CLUS_2                       10                            135
  CLUS_3                        5                            104
D14V11, multiclass
D14V12, multiclass
        clus
vv       AMP PEAK 14(13Q33.3) CNV AMP PEAK 14(13Q33.3) WILD-TYPE
  CLUS_1                        2                             40
  CLUS_2                        9                             96
  CLUS_3                        4                            117

Clustering(15) Variable = Amp Peak 15(17q25.1)
D15V1, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        3                              7
  CLUS_3                        0                              8
D15V2, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        1                              6
  CLUS_2                        0                              6
  CLUS_3                        0                             10
  CLUS_4                        2                              2
D15V3, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        1                             51
  CLUS_2                        1                             56
  CLUS_3                       12                             42
  CLUS_4                        2                            104
D15V4, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                       11                            111
  CLUS_2                        2                             40
  CLUS_3                        3                             63
  CLUS_4                        0                             34
D15V5, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        4                             48
  CLUS_2                        7                             55
  CLUS_3                        2                             66
  CLUS_4                        3                             71
D15V6, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                        8                            121
  CLUS_3                        8                            111
D15V7, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        8                             86
  CLUS_2                        4                             74
  CLUS_3                        4                             93
D15V8, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        2                             34
  CLUS_2                       10                            131
  CLUS_3                        4                             88
D15V9, multiclass
D15V10, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        1                             13
  CLUS_2                       11                            134
  CLUS_3                        4                            105
D15V11, multiclass
D15V12, multiclass
        clus
vv       AMP PEAK 15(17Q25.1) CNV AMP PEAK 15(17Q25.1) WILD-TYPE
  CLUS_1                        3                             39
  CLUS_2                        7                             98
  CLUS_3                        6                            115

Clustering(16) Variable = Amp Peak 16(18q23)
D16V1, multiclass
[1] "Remove cluster labels:" "AMP PEAK 16(18Q23) CNV"
clus
      AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE 
                           2                           25 
                  TCGA-CS-4942                   TCGA-CS-4943 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-CS-4944                   TCGA-CS-5390 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-CS-5394                   TCGA-CS-5395 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-CS-5396                   TCGA-DB-5270 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5273                   TCGA-DB-5274 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5275                   TCGA-DB-5276 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5278                   TCGA-DB-5280 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5281                   TCGA-DH-5140 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DH-5141                   TCGA-DH-5142 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DH-5143                   TCGA-DH-5144 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-E1-5302                   TCGA-E1-5303 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-E1-5311                   TCGA-E1-5318 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-E1-5322 
"AMP PEAK 16(18Q23) WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "AMP PEAK 16(18Q23) CNV"
clus
      AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE 
                           2                           25 
                  TCGA-CS-4942                   TCGA-CS-4943 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-CS-4944                   TCGA-CS-5390 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-CS-5394                   TCGA-CS-5395 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-CS-5396                   TCGA-DB-5270 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5273                   TCGA-DB-5274 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5275                   TCGA-DB-5276 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5278                   TCGA-DB-5280 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DB-5281                   TCGA-DH-5140 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DH-5141                   TCGA-DH-5142 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-DH-5143                   TCGA-DH-5144 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-E1-5302                   TCGA-E1-5303 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-E1-5311                   TCGA-E1-5318 
"AMP PEAK 16(18Q23) WILD-TYPE" "AMP PEAK 16(18Q23) WILD-TYPE" 
                  TCGA-E1-5322 
"AMP PEAK 16(18Q23) WILD-TYPE" 
D16V3, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      1                           51
  CLUS_2                      2                           55
  CLUS_3                      8                           46
  CLUS_4                      1                          105
D16V4, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                     10                          112
  CLUS_2                      2                           40
  CLUS_3                      0                           66
  CLUS_4                      0                           34
D16V5, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      3                           49
  CLUS_2                      8                           54
  CLUS_3                      0                           68
  CLUS_4                      0                           74
D16V6, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      0                            8
  CLUS_2                      6                          123
  CLUS_3                      5                          114
D16V7, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      8                           86
  CLUS_2                      4                           74
  CLUS_3                      0                           97
D16V8, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      0                           36
  CLUS_2                     12                          129
  CLUS_3                      0                           92
D16V9, multiclass
D16V10, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      1                           13
  CLUS_2                      8                          137
  CLUS_3                      3                          106
D16V11, multiclass
D16V12, multiclass
        clus
vv       AMP PEAK 16(18Q23) CNV AMP PEAK 16(18Q23) WILD-TYPE
  CLUS_1                      3                           39
  CLUS_2                      7                           98
  CLUS_3                      2                          119

Clustering(17) Variable = Amp Peak 17(19p13.3)
D17V1, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        5                              5
  CLUS_3                        2                              6
D17V2, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                        4                              3
  CLUS_2                        1                              5
  CLUS_3                        2                              8
  CLUS_4                        1                              3
D17V3, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                        2                             50
  CLUS_2                       17                             40
  CLUS_3                        8                             46
  CLUS_4                       33                             73
D17V4, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                       10                            112
  CLUS_2                       14                             28
  CLUS_3                       29                             37
  CLUS_4                        3                             31
D17V5, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                       11                             41
  CLUS_2                       16                             46
  CLUS_3                       14                             54
  CLUS_4                       15                             59
D17V6, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                       31                             98
  CLUS_3                       24                             95
D17V7, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                       18                             76
  CLUS_2                       19                             59
  CLUS_3                       23                             74
D17V8, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                       15                             21
  CLUS_2                       25                            116
  CLUS_3                       20                             72
D17V9, multiclass
D17V10, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                        4                             10
  CLUS_2                       27                            118
  CLUS_3                       29                             80
D17V11, multiclass
D17V12, multiclass
        clus
vv       AMP PEAK 17(19P13.3) CNV AMP PEAK 17(19P13.3) WILD-TYPE
  CLUS_1                       15                             27
  CLUS_2                       15                             90
  CLUS_3                       30                             91

Clustering(18) Variable = Amp Peak 18(19q13.2)
D18V1, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        2                              7
  CLUS_2                        0                             10
  CLUS_3                        1                              7
D18V2, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        0                              6
  CLUS_3                        3                              7
  CLUS_4                        0                              4
D18V3, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        0                             52
  CLUS_2                       14                             43
  CLUS_3                        3                             51
  CLUS_4                        2                            104
D18V4, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        6                            116
  CLUS_2                       11                             31
  CLUS_3                        0                             66
  CLUS_4                        1                             33
D18V5, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        4                             48
  CLUS_2                        8                             54
  CLUS_3                        3                             65
  CLUS_4                        1                             73
D18V6, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       11                            118
  CLUS_3                        5                            114
D18V7, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                       15                             79
  CLUS_2                        3                             75
  CLUS_3                        1                             96
D18V8, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        0                             36
  CLUS_2                       17                            124
  CLUS_3                        2                             90
D18V9, multiclass
D18V10, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                        3                             11
  CLUS_2                       14                            131
  CLUS_3                        2                            107
D18V11, multiclass
D18V12, multiclass
        clus
vv       AMP PEAK 18(19Q13.2) CNV AMP PEAK 18(19Q13.2) WILD-TYPE
  CLUS_1                       11                             31
  CLUS_2                        6                             99
  CLUS_3                        2                            119

Clustering(19) Variable = Amp Peak 19(Xp22.33)
D19V1, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 19(XP22.33) CNV"
clus
      AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE 
                             2                             25 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5318 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-E1-5322 
"AMP PEAK 19(XP22.33) WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:"   "AMP PEAK 19(XP22.33) CNV"
clus
      AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE 
                             2                             25 
                    TCGA-CS-4942                     TCGA-CS-4943 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-CS-4944                     TCGA-CS-5390 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-CS-5394                     TCGA-CS-5395 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-CS-5396                     TCGA-DB-5270 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5273                     TCGA-DB-5274 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5275                     TCGA-DB-5276 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5278                     TCGA-DB-5280 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DB-5281                     TCGA-DH-5140 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DH-5141                     TCGA-DH-5142 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-DH-5143                     TCGA-DH-5144 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-E1-5303                     TCGA-E1-5304 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-E1-5311                     TCGA-E1-5318 
"AMP PEAK 19(XP22.33) WILD-TYPE" "AMP PEAK 19(XP22.33) WILD-TYPE" 
                    TCGA-E1-5322 
"AMP PEAK 19(XP22.33) WILD-TYPE" 
D19V3, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        7                             45
  CLUS_2                        6                             51
  CLUS_3                        5                             49
  CLUS_4                        0                            106
D19V4, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                       14                            108
  CLUS_2                        4                             38
  CLUS_3                        0                             66
  CLUS_4                        0                             34
D19V5, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        3                             49
  CLUS_2                        7                             55
  CLUS_3                        3                             65
  CLUS_4                        3                             71
D19V6, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       11                            118
  CLUS_3                        5                            114
D19V7, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        9                             85
  CLUS_2                        6                             72
  CLUS_3                        3                             94
D19V8, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        0                             36
  CLUS_2                       15                            126
  CLUS_3                        3                             89
D19V9, multiclass
D19V10, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        4                             10
  CLUS_2                       10                            135
  CLUS_3                        4                            105
D19V11, multiclass
D19V12, multiclass
        clus
vv       AMP PEAK 19(XP22.33) CNV AMP PEAK 19(XP22.33) WILD-TYPE
  CLUS_1                        5                             37
  CLUS_2                        7                             98
  CLUS_3                        6                            115

Clustering(20) Variable = Amp Peak 20(Xp11.22)
D20V1, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        1                              8
  CLUS_2                        1                              9
  CLUS_3                        2                              6
D20V2, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        1                              6
  CLUS_2                        1                              5
  CLUS_3                        1                              9
  CLUS_4                        1                              3
D20V3, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                       19                             33
  CLUS_2                        4                             53
  CLUS_3                       13                             41
  CLUS_4                        2                            104
D20V4, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                       32                             90
  CLUS_2                        4                             38
  CLUS_3                        1                             65
  CLUS_4                        1                             33
D20V5, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        5                             47
  CLUS_2                       14                             48
  CLUS_3                       13                             55
  CLUS_4                        5                             69
D20V6, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       24                            105
  CLUS_3                       13                            106
D20V7, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                       18                             76
  CLUS_2                       12                             66
  CLUS_3                        8                             89
D20V8, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        1                             35
  CLUS_2                       31                            110
  CLUS_3                        6                             86
D20V9, multiclass
D20V10, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        4                             10
  CLUS_2                       24                            121
  CLUS_3                       10                             99
D20V11, multiclass
D20V12, multiclass
        clus
vv       AMP PEAK 20(XP11.22) CNV AMP PEAK 20(XP11.22) WILD-TYPE
  CLUS_1                        6                             36
  CLUS_2                       22                             83
  CLUS_3                       10                            111

Clustering(21) Variable = Del Peak  1(1p36.31)
D21V1, 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
D21V2, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        7                              0
  CLUS_2                        2                              4
  CLUS_3                        0                             10
  CLUS_4                        1                              3
D21V3, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        5                             47
  CLUS_2                        9                             48
  CLUS_3                       15                             39
  CLUS_4                       67                             39
D21V4, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        8                            114
  CLUS_2                        9                             33
  CLUS_3                       66                              0
  CLUS_4                        9                             25
D21V5, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        8                             44
  CLUS_2                       21                             41
  CLUS_3                       29                             39
  CLUS_4                       36                             38
D21V6, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        4                              4
  CLUS_2                       44                             85
  CLUS_3                       46                             73
D21V7, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                       16                             78
  CLUS_2                       34                             44
  CLUS_3                       46                             51
D21V8, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                       36                              0
  CLUS_2                       21                            120
  CLUS_3                       39                             53
D21V9, multiclass
D21V10, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        2                             12
  CLUS_2                       40                            105
  CLUS_3                       54                             55
D21V11, multiclass
D21V12, multiclass
        clus
vv       DEL PEAK  1(1P36.31) CNV DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                        9                             33
  CLUS_2                       27                             78
  CLUS_3                       60                             61

Clustering(22) Variable = Del Peak  2(1p32.3)
D22V1, 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
D22V2, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       7                             0
  CLUS_2                       2                             4
  CLUS_3                       1                             9
  CLUS_4                       0                             4
D22V3, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       4                            48
  CLUS_2                       5                            52
  CLUS_3                      12                            42
  CLUS_4                      67                            39
D22V4, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       4                           118
  CLUS_2                       6                            36
  CLUS_3                      66                             0
  CLUS_4                       9                            25
D22V5, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       8                            44
  CLUS_2                      16                            46
  CLUS_3                      28                            40
  CLUS_4                      35                            39
D22V6, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       4                             4
  CLUS_2                      38                            91
  CLUS_3                      45                            74
D22V7, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       9                            85
  CLUS_2                      34                            44
  CLUS_3                      45                            52
D22V8, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                      36                             0
  CLUS_2                      14                           127
  CLUS_3                      38                            54
D22V9, multiclass
D22V10, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       1                            13
  CLUS_2                      35                           110
  CLUS_3                      52                            57
D22V11, multiclass
D22V12, multiclass
        clus
vv       DEL PEAK  2(1P32.3) CNV DEL PEAK  2(1P32.3) WILD-TYPE
  CLUS_1                       5                            37
  CLUS_2                      24                            81
  CLUS_3                      59                            62

Clustering(23) Variable = Del Peak  3(1q43)
D23V1, 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" 
D23V2, 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" 
D23V3, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     6                          46
  CLUS_2                     3                          54
  CLUS_3                     4                          50
  CLUS_4                     2                         104
D23V4, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                    10                         112
  CLUS_2                     3                          39
  CLUS_3                     1                          65
  CLUS_4                     1                          33
D23V5, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     2                          50
  CLUS_2                     8                          54
  CLUS_3                     2                          66
  CLUS_4                     3                          71
D23V6, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     0                           8
  CLUS_2                    10                         119
  CLUS_3                     5                         114
D23V7, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     5                          89
  CLUS_2                     5                          73
  CLUS_3                     5                          92
D23V8, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     0                          36
  CLUS_2                    11                         130
  CLUS_3                     4                          88
D23V9, multiclass
D23V10, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     0                          14
  CLUS_2                    10                         135
  CLUS_3                     5                         104
D23V11, multiclass
D23V12, multiclass
        clus
vv       DEL PEAK  3(1Q43) CNV DEL PEAK  3(1Q43) WILD-TYPE
  CLUS_1                     2                          40
  CLUS_2                     8                          97
  CLUS_3                     5                         116

Clustering(24) Variable = Del Peak  4(2p25.3)
D24V1, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       0                            10
  CLUS_3                       1                             7
D24V2, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       0                             6
  CLUS_3                       2                             8
  CLUS_4                       1                             3
D24V3, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       9                            43
  CLUS_2                       2                            55
  CLUS_3                      12                            42
  CLUS_4                       1                           105
D24V4, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                      19                           103
  CLUS_2                       3                            39
  CLUS_3                       1                            65
  CLUS_4                       1                            33
D24V5, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       7                            45
  CLUS_2                       8                            54
  CLUS_3                       3                            65
  CLUS_4                       5                            69
D24V6, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      12                           117
  CLUS_3                      11                           108
D24V7, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                      10                            84
  CLUS_2                       8                            70
  CLUS_3                       6                            91
D24V8, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       1                            35
  CLUS_2                      18                           123
  CLUS_3                       5                            87
D24V9, multiclass
D24V10, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       1                            13
  CLUS_2                      15                           130
  CLUS_3                       8                           101
D24V11, multiclass
D24V12, multiclass
        clus
vv       DEL PEAK  4(2P25.3) CNV DEL PEAK  4(2P25.3) WILD-TYPE
  CLUS_1                       2                            40
  CLUS_2                      14                            91
  CLUS_3                       8                           113

Clustering(25) Variable = Del Peak  5(2q37.1)
D25V1, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       1                             9
  CLUS_3                       2                             6
D25V2, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       1                             5
  CLUS_3                       1                             9
  CLUS_4                       2                             2
D25V3, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                      14                            38
  CLUS_2                       9                            48
  CLUS_3                       9                            45
  CLUS_4                       1                           105
D25V4, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                      28                            94
  CLUS_2                       2                            40
  CLUS_3                       1                            65
  CLUS_4                       2                            32
D25V5, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       7                            45
  CLUS_2                      16                            46
  CLUS_3                       7                            61
  CLUS_4                       3                            71
D25V6, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      24                           105
  CLUS_3                       9                           110
D25V7, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                      18                            76
  CLUS_2                       9                            69
  CLUS_3                       6                            91
D25V8, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       1                            35
  CLUS_2                      27                           114
  CLUS_3                       5                            87
D25V9, multiclass
D25V10, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       2                            12
  CLUS_2                      25                           120
  CLUS_3                       6                           103
D25V11, multiclass
D25V12, multiclass
        clus
vv       DEL PEAK  5(2Q37.1) CNV DEL PEAK  5(2Q37.1) WILD-TYPE
  CLUS_1                       4                            38
  CLUS_2                      22                            83
  CLUS_3                       7                           114

Clustering(26) Variable = Del Peak  6(2q37.3)
D26V1, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       2                             7
  CLUS_2                       1                             9
  CLUS_3                       4                             4
D26V2, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       3                             3
  CLUS_3                       2                             8
  CLUS_4                       2                             2
D26V3, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                      15                            37
  CLUS_2                      10                            47
  CLUS_3                      12                            42
  CLUS_4                       3                           103
D26V4, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                      35                            87
  CLUS_2                       1                            41
  CLUS_3                       2                            64
  CLUS_4                       2                            32
D26V5, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       8                            44
  CLUS_2                      17                            45
  CLUS_3                      10                            58
  CLUS_4                       5                            69
D26V6, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      28                           101
  CLUS_3                      12                           107
D26V7, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                      18                            76
  CLUS_2                      12                            66
  CLUS_3                      10                            87
D26V8, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       1                            35
  CLUS_2                      30                           111
  CLUS_3                       9                            83
D26V9, multiclass
D26V10, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       2                            12
  CLUS_2                      27                           118
  CLUS_3                      11                            98
D26V11, multiclass
D26V12, multiclass
        clus
vv       DEL PEAK  6(2Q37.3) CNV DEL PEAK  6(2Q37.3) WILD-TYPE
  CLUS_1                       3                            39
  CLUS_2                      28                            77
  CLUS_3                       9                           112

Clustering(27) Variable = Del Peak  7(3p21.1)
D27V1, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             8
  CLUS_3                       1                             7
D27V2, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       0                             6
  CLUS_3                       1                             9
  CLUS_4                       3                             1
D27V3, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       8                            44
  CLUS_2                       4                            53
  CLUS_3                      15                            39
  CLUS_4                       1                           105
D27V4, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                      20                           102
  CLUS_2                       4                            38
  CLUS_3                       2                            64
  CLUS_4                       1                            33
D27V5, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       4                            48
  CLUS_2                      16                            46
  CLUS_3                       3                            65
  CLUS_4                       4                            70
D27V6, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      16                           113
  CLUS_3                       9                           110
D27V7, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                      17                            77
  CLUS_2                       5                            73
  CLUS_3                       6                            91
D27V8, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       1                            35
  CLUS_2                      23                           118
  CLUS_3                       4                            88
D27V9, multiclass
D27V10, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       1                            13
  CLUS_2                      21                           124
  CLUS_3                       6                           103
D27V11, multiclass
D27V12, multiclass
        clus
vv       DEL PEAK  7(3P21.1) CNV DEL PEAK  7(3P21.1) WILD-TYPE
  CLUS_1                       7                            35
  CLUS_2                      15                            90
  CLUS_3                       6                           115

Clustering(28) Variable = Del Peak  8(4q35.2)
D28V1, 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
D28V2, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       2                             5
  CLUS_2                       2                             4
  CLUS_3                       4                             6
  CLUS_4                       3                             1
D28V3, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      16                            36
  CLUS_2                       4                            53
  CLUS_3                      32                            22
  CLUS_4                      24                            82
D28V4, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      43                            79
  CLUS_2                       2                            40
  CLUS_3                      28                            38
  CLUS_4                       3                            31
D28V5, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       8                            44
  CLUS_2                      20                            42
  CLUS_3                      24                            44
  CLUS_4                      22                            52
D28V6, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       5                             3
  CLUS_2                      39                            90
  CLUS_3                      30                            89
D28V7, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      16                            78
  CLUS_2                      31                            47
  CLUS_3                      29                            68
D28V8, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                      18                            18
  CLUS_2                      33                           108
  CLUS_3                      25                            67
D28V9, multiclass
D28V10, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       2                            12
  CLUS_2                      39                           106
  CLUS_3                      35                            74
D28V11, multiclass
D28V12, multiclass
        clus
vv       DEL PEAK  8(4Q35.2) CNV DEL PEAK  8(4Q35.2) WILD-TYPE
  CLUS_1                       4                            38
  CLUS_2                      32                            73
  CLUS_3                      40                            81

Clustering(29) Variable = Del Peak  9(5q35.2)
D29V1, 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
D29V2, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       2                             4
  CLUS_3                       1                             9
  CLUS_4                       3                             1
D29V3, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                      13                            39
  CLUS_2                       1                            56
  CLUS_3                      17                            37
  CLUS_4                       3                           103
D29V4, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                      24                            98
  CLUS_2                       5                            37
  CLUS_3                       1                            65
  CLUS_4                       4                            30
D29V5, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       7                            45
  CLUS_2                      14                            48
  CLUS_3                       6                            62
  CLUS_4                       7                            67
D29V6, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                      18                           111
  CLUS_3                      15                           104
D29V7, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                      18                            76
  CLUS_2                       6                            72
  CLUS_3                      10                            87
D29V8, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       0                            36
  CLUS_2                      24                           117
  CLUS_3                      10                            82
D29V9, multiclass
D29V10, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       3                            11
  CLUS_2                      19                           126
  CLUS_3                      12                            97
D29V11, multiclass
D29V12, multiclass
        clus
vv       DEL PEAK  9(5Q35.2) CNV DEL PEAK  9(5Q35.2) WILD-TYPE
  CLUS_1                       7                            35
  CLUS_2                      16                            89
  CLUS_3                      11                           110

Clustering(30) Variable = Del Peak 10(6p25.3)
D30V1, multiclass
[1] "Remove cluster labels:"  "DEL PEAK 10(6P25.3) CNV"
clus
      DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE 
                            1                            26 
                   TCGA-CS-4942                    TCGA-CS-4943 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5395 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-CS-5396                    TCGA-DB-5270 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5273                    TCGA-DB-5274 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5275                    TCGA-DB-5276 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5278                    TCGA-DB-5280 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5281                    TCGA-DH-5140 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DH-5141                    TCGA-DH-5142 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DH-5143                    TCGA-DH-5144 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-E1-5302                    TCGA-E1-5303 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-E1-5304                    TCGA-E1-5311 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-E1-5318                    TCGA-E1-5322 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:"  "DEL PEAK 10(6P25.3) CNV"
clus
      DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE 
                            1                            26 
                   TCGA-CS-4942                    TCGA-CS-4943 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-CS-4944                    TCGA-CS-5390 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-CS-5394                    TCGA-CS-5395 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-CS-5396                    TCGA-DB-5270 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5273                    TCGA-DB-5274 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5275                    TCGA-DB-5276 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5278                    TCGA-DB-5280 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DB-5281                    TCGA-DH-5140 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DH-5141                    TCGA-DH-5142 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-DH-5143                    TCGA-DH-5144 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-E1-5302                    TCGA-E1-5303 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-E1-5304                    TCGA-E1-5311 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
                   TCGA-E1-5318                    TCGA-E1-5322 
"DEL PEAK 10(6P25.3) WILD-TYPE" "DEL PEAK 10(6P25.3) WILD-TYPE" 
D30V3, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                       4                            48
  CLUS_2                       8                            49
  CLUS_3                      10                            44
  CLUS_4                       6                           100
D30V4, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                      15                           107
  CLUS_2                       6                            36
  CLUS_3                       4                            62
  CLUS_4                       2                            32
D30V5, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                       6                            46
  CLUS_2                      10                            52
  CLUS_3                       3                            65
  CLUS_4                       8                            66
D30V6, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                       0                             8
  CLUS_2                      15                           114
  CLUS_3                      12                           107
D30V7, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                      12                            82
  CLUS_2                       9                            69
  CLUS_3                       7                            90
D30V8, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                       3                            33
  CLUS_2                      19                           122
  CLUS_3                       6                            86
D30V9, multiclass
D30V10, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                       2                            12
  CLUS_2                      16                           129
  CLUS_3                      10                            99
D30V11, multiclass
D30V12, multiclass
        clus
vv       DEL PEAK 10(6P25.3) CNV DEL PEAK 10(6P25.3) WILD-TYPE
  CLUS_1                       8                            34
  CLUS_2                      11                            94
  CLUS_3                       9                           112

Clustering(31) Variable = Del Peak 11(6q24.3)
D31V1, 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
D31V2, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       0                             6
  CLUS_3                       3                             7
  CLUS_4                       0                             4
D31V3, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       6                            46
  CLUS_2                      12                            45
  CLUS_3                      19                            35
  CLUS_4                       8                            98
D31V4, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                      29                            93
  CLUS_2                      10                            32
  CLUS_3                       3                            63
  CLUS_4                       3                            31
D31V5, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       7                            45
  CLUS_2                      16                            46
  CLUS_3                       8                            60
  CLUS_4                      11                            63
D31V6, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       1                             7
  CLUS_2                      26                           103
  CLUS_3                      15                           104
D31V7, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                      18                            76
  CLUS_2                      13                            65
  CLUS_3                      14                            83
D31V8, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       2                            34
  CLUS_2                      29                           112
  CLUS_3                      14                            78
D31V9, multiclass
D31V10, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       2                            12
  CLUS_2                      28                           117
  CLUS_3                      15                            94
D31V11, multiclass
D31V12, multiclass
        clus
vv       DEL PEAK 11(6Q24.3) CNV DEL PEAK 11(6Q24.3) WILD-TYPE
  CLUS_1                       8                            34
  CLUS_2                      23                            82
  CLUS_3                      14                           107

Clustering(32) Variable = Del Peak 12(9p21.3)
D32V1, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       4                             6
  CLUS_3                       3                             5
D32V2, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                       1                             6
  CLUS_2                       1                             5
  CLUS_3                       2                             8
  CLUS_4                       4                             0
D32V3, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                      13                            39
  CLUS_2                      38                            19
  CLUS_3                      30                            24
  CLUS_4                      18                            88
D32V4, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                      49                            73
  CLUS_2                      30                            12
  CLUS_3                      13                            53
  CLUS_4                       5                            29
D32V5, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                      11                            41
  CLUS_2                      38                            24
  CLUS_3                      26                            42
  CLUS_4                      18                            56
D32V6, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      63                            66
  CLUS_3                      28                            91
D32V7, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                      45                            49
  CLUS_2                      24                            54
  CLUS_3                      30                            67
D32V8, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                      10                            26
  CLUS_2                      64                            77
  CLUS_3                      25                            67
D32V9, multiclass
D32V10, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                       7                             7
  CLUS_2                      58                            87
  CLUS_3                      34                            75
D32V11, multiclass
D32V12, multiclass
        clus
vv       DEL PEAK 12(9P21.3) CNV DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                      27                            15
  CLUS_2                      38                            67
  CLUS_3                      34                            87

Clustering(33) Variable = Del Peak 13(10q26.3)
D33V1, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                        0                              9
  CLUS_2                        2                              8
  CLUS_3                        3                              5
D33V2, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        1                              5
  CLUS_3                        1                              9
  CLUS_4                        3                              1
D33V3, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                       14                             38
  CLUS_2                       38                             19
  CLUS_3                       25                             29
  CLUS_4                        4                            102
D33V4, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                       36                             86
  CLUS_2                       37                              5
  CLUS_3                        3                             63
  CLUS_4                        4                             30
D33V5, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                       13                             39
  CLUS_2                       36                             26
  CLUS_3                       13                             55
  CLUS_4                       11                             63
D33V6, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       51                             78
  CLUS_3                       20                             99
D33V7, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                       50                             44
  CLUS_2                       14                             64
  CLUS_3                       17                             80
D33V8, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                        1                             35
  CLUS_2                       64                             77
  CLUS_3                       16                             76
D33V9, multiclass
D33V10, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                       10                              4
  CLUS_2                       53                             92
  CLUS_3                       18                             91
D33V11, multiclass
D33V12, multiclass
        clus
vv       DEL PEAK 13(10Q26.3) CNV DEL PEAK 13(10Q26.3) WILD-TYPE
  CLUS_1                       32                             10
  CLUS_2                       29                             76
  CLUS_3                       20                            101

Clustering(34) Variable = Del Peak 14(11p15.5)
D34V1, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                        3                              6
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D34V2, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        0                              6
  CLUS_3                        3                              7
  CLUS_4                        4                              0
D34V3, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                       23                             29
  CLUS_2                        8                             49
  CLUS_3                       20                             34
  CLUS_4                        6                            100
D34V4, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                       46                             76
  CLUS_2                        6                             36
  CLUS_3                        0                             66
  CLUS_4                        5                             29
D34V5, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                       13                             39
  CLUS_2                       18                             44
  CLUS_3                        9                             59
  CLUS_4                       15                             59
D34V6, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                        1                              7
  CLUS_2                       27                            102
  CLUS_3                       27                             92
D34V7, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                       31                             63
  CLUS_2                       10                             68
  CLUS_3                       16                             81
D34V8, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                        0                             36
  CLUS_2                       42                             99
  CLUS_3                       15                             77
D34V9, multiclass
D34V10, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                        4                             10
  CLUS_2                       34                            111
  CLUS_3                       19                             90
D34V11, multiclass
D34V12, multiclass
        clus
vv       DEL PEAK 14(11P15.5) CNV DEL PEAK 14(11P15.5) WILD-TYPE
  CLUS_1                        8                             34
  CLUS_2                       27                             78
  CLUS_3                       22                             99

Clustering(35) Variable = Del Peak 15(11q25)
D35V1, multiclass
[1] "Remove cluster labels:" "DEL PEAK 15(11Q25) CNV"
clus
      DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE 
                           1                           26 
                  TCGA-CS-4942                   TCGA-CS-4943 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-CS-4944                   TCGA-CS-5390 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-CS-5394                   TCGA-CS-5395 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-CS-5396                   TCGA-DB-5270 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5273                   TCGA-DB-5274 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5275                   TCGA-DB-5276 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5277                   TCGA-DB-5278 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5280                   TCGA-DB-5281 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DH-5141                   TCGA-DH-5142 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DH-5143                   TCGA-DH-5144 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-E1-5302                   TCGA-E1-5303 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-E1-5304                   TCGA-E1-5311 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-E1-5318                   TCGA-E1-5322 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
D35V2, multiclass
[1] "Remove cluster labels:" "DEL PEAK 15(11Q25) CNV"
clus
      DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE 
                           1                           26 
                  TCGA-CS-4942                   TCGA-CS-4943 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-CS-4944                   TCGA-CS-5390 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-CS-5394                   TCGA-CS-5395 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-CS-5396                   TCGA-DB-5270 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5273                   TCGA-DB-5274 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5275                   TCGA-DB-5276 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5277                   TCGA-DB-5278 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DB-5280                   TCGA-DB-5281 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DH-5141                   TCGA-DH-5142 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-DH-5143                   TCGA-DH-5144 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-E1-5302                   TCGA-E1-5303 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-E1-5304                   TCGA-E1-5311 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
                  TCGA-E1-5318                   TCGA-E1-5322 
"DEL PEAK 15(11Q25) WILD-TYPE" "DEL PEAK 15(11Q25) WILD-TYPE" 
D35V3, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                      6                           46
  CLUS_2                      4                           53
  CLUS_3                     10                           44
  CLUS_4                      1                          105
D35V4, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                     13                          109
  CLUS_2                      6                           36
  CLUS_3                      0                           66
  CLUS_4                      2                           32
D35V5, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                      4                           48
  CLUS_2                      8                           54
  CLUS_3                      4                           64
  CLUS_4                      4                           70
D35V6, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                      0                            8
  CLUS_2                     13                          116
  CLUS_3                      7                          112
D35V7, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                     12                           82
  CLUS_2                      4                           74
  CLUS_3                      5                           92
D35V8, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                      0                           36
  CLUS_2                     16                          125
  CLUS_3                      5                           87
D35V9, multiclass
D35V10, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                      2                           12
  CLUS_2                     14                          131
  CLUS_3                      5                          104
D35V11, multiclass
D35V12, multiclass
        clus
vv       DEL PEAK 15(11Q25) CNV DEL PEAK 15(11Q25) WILD-TYPE
  CLUS_1                      5                           37
  CLUS_2                     10                           95
  CLUS_3                      6                          115

Clustering(36) Variable = Del Peak 16(12q12)
D36V1, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      1                            8
  CLUS_2                      1                            9
  CLUS_3                      1                            7
D36V2, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      0                            7
  CLUS_2                      0                            6
  CLUS_3                      1                            9
  CLUS_4                      2                            2
D36V3, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                     18                           34
  CLUS_2                      4                           53
  CLUS_3                      8                           46
  CLUS_4                      5                          101
D36V4, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                     27                           95
  CLUS_2                      3                           39
  CLUS_3                      2                           64
  CLUS_4                      3                           31
D36V5, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      5                           47
  CLUS_2                      9                           53
  CLUS_3                      6                           62
  CLUS_4                     12                           62
D36V6, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      1                            7
  CLUS_2                     15                          114
  CLUS_3                     16                          103
D36V7, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                     15                           79
  CLUS_2                      5                           73
  CLUS_3                     15                           82
D36V8, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      0                           36
  CLUS_2                     23                          118
  CLUS_3                     12                           80
D36V9, multiclass
D36V10, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      1                           13
  CLUS_2                     19                          126
  CLUS_3                     15                           94
D36V11, multiclass
D36V12, multiclass
        clus
vv       DEL PEAK 16(12Q12) CNV DEL PEAK 16(12Q12) WILD-TYPE
  CLUS_1                      6                           36
  CLUS_2                     11                           94
  CLUS_3                     18                          103

Clustering(37) Variable = Del Peak 17(13q14.2)
D37V1, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                        5                              4
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D37V2, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        0                              6
  CLUS_3                        5                              5
  CLUS_4                        4                              0
D37V3, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                       19                             33
  CLUS_2                        8                             49
  CLUS_3                       47                              7
  CLUS_4                        3                            103
D37V4, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                       45                             77
  CLUS_2                       15                             27
  CLUS_3                       12                             54
  CLUS_4                        5                             29
D37V5, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                        9                             43
  CLUS_2                       26                             36
  CLUS_3                       18                             50
  CLUS_4                       20                             54
D37V6, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                        3                              5
  CLUS_2                       37                             92
  CLUS_3                       33                             86
D37V7, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                       32                             62
  CLUS_2                       21                             57
  CLUS_3                       24                             73
D37V8, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                        8                             28
  CLUS_2                       48                             93
  CLUS_3                       21                             71
D37V9, multiclass
D37V10, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                        6                              8
  CLUS_2                       44                            101
  CLUS_3                       27                             82
D37V11, multiclass
D37V12, multiclass
        clus
vv       DEL PEAK 17(13Q14.2) CNV DEL PEAK 17(13Q14.2) WILD-TYPE
  CLUS_1                       10                             32
  CLUS_2                       36                             69
  CLUS_3                       31                             90

Clustering(38) Variable = Del Peak 18(13q21.2)
D38V1, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                        5                              4
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D38V2, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        0                              6
  CLUS_3                        5                              5
  CLUS_4                        4                              0
D38V3, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                       20                             32
  CLUS_2                       10                             47
  CLUS_3                       47                              7
  CLUS_4                        3                            103
D38V4, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                       46                             76
  CLUS_2                       17                             25
  CLUS_3                       12                             54
  CLUS_4                        5                             29
D38V5, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                       10                             42
  CLUS_2                       28                             34
  CLUS_3                       18                             50
  CLUS_4                       20                             54
D38V6, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                        3                              5
  CLUS_2                       40                             89
  CLUS_3                       33                             86
D38V7, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                       35                             59
  CLUS_2                       21                             57
  CLUS_3                       24                             73
D38V8, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                        8                             28
  CLUS_2                       51                             90
  CLUS_3                       21                             71
D38V9, multiclass
D38V10, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                        6                              8
  CLUS_2                       47                             98
  CLUS_3                       27                             82
D38V11, multiclass
D38V12, multiclass
        clus
vv       DEL PEAK 18(13Q21.2) CNV DEL PEAK 18(13Q21.2) WILD-TYPE
  CLUS_1                       12                             30
  CLUS_2                       37                             68
  CLUS_3                       31                             90

Clustering(39) Variable = Del Peak 19(13q22.1)
D39V1, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                        4                              5
  CLUS_2                        3                              7
  CLUS_3                        1                              7
D39V2, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        0                              6
  CLUS_3                        4                              6
  CLUS_4                        4                              0
D39V3, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                       18                             34
  CLUS_2                        9                             48
  CLUS_3                       45                              9
  CLUS_4                        5                            101
D39V4, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                       43                             79
  CLUS_2                       16                             26
  CLUS_3                       13                             53
  CLUS_4                        5                             29
D39V5, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                        9                             43
  CLUS_2                       28                             34
  CLUS_3                       17                             51
  CLUS_4                       20                             54
D39V6, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                        3                              5
  CLUS_2                       38                             91
  CLUS_3                       33                             86
D39V7, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                       31                             63
  CLUS_2                       22                             56
  CLUS_3                       24                             73
D39V8, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                        8                             28
  CLUS_2                       48                             93
  CLUS_3                       21                             71
D39V9, multiclass
D39V10, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                        5                              9
  CLUS_2                       45                            100
  CLUS_3                       27                             82
D39V11, multiclass
D39V12, multiclass
        clus
vv       DEL PEAK 19(13Q22.1) CNV DEL PEAK 19(13Q22.1) WILD-TYPE
  CLUS_1                       11                             31
  CLUS_2                       35                             70
  CLUS_3                       31                             90

Clustering(40) Variable = Del Peak 20(13q34)
D40V1, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                      2                            7
  CLUS_2                      2                            8
  CLUS_3                      0                            8
D40V2, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                      0                            7
  CLUS_2                      0                            6
  CLUS_3                      2                            8
  CLUS_4                      2                            2
D40V3, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                     15                           37
  CLUS_2                      6                           51
  CLUS_3                     33                           21
  CLUS_4                      3                          103
D40V4, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                     28                           94
  CLUS_2                     13                           29
  CLUS_3                     11                           55
  CLUS_4                      5                           29
D40V5, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                      7                           45
  CLUS_2                     20                           42
  CLUS_3                     12                           56
  CLUS_4                     15                           59
D40V6, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                      3                            5
  CLUS_2                     27                          102
  CLUS_3                     24                           95
D40V7, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                     24                           70
  CLUS_2                     15                           63
  CLUS_3                     18                           79
D40V8, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                      7                           29
  CLUS_2                     36                          105
  CLUS_3                     14                           78
D40V9, multiclass
D40V10, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                      4                           10
  CLUS_2                     35                          110
  CLUS_3                     18                           91
D40V11, multiclass
D40V12, multiclass
        clus
vv       DEL PEAK 20(13Q34) CNV DEL PEAK 20(13Q34) WILD-TYPE
  CLUS_1                     10                           32
  CLUS_2                     24                           81
  CLUS_3                     23                           98

Clustering(41) Variable = Del Peak 21(14q24.3)
D41V1, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        4                              5
  CLUS_2                        2                              8
  CLUS_3                        1                              7
D41V2, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        0                              7
  CLUS_2                        1                              5
  CLUS_3                        4                              6
  CLUS_4                        2                              2
D41V3, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        7                             45
  CLUS_2                       14                             43
  CLUS_3                       25                             29
  CLUS_4                       15                             91
D41V4, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                       32                             90
  CLUS_2                       14                             28
  CLUS_3                        9                             57
  CLUS_4                        5                             29
D41V5, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        6                             46
  CLUS_2                       23                             39
  CLUS_3                       18                             50
  CLUS_4                       11                             63
D41V6, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        2                              6
  CLUS_2                       38                             91
  CLUS_3                       18                            101
D41V7, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                       32                             62
  CLUS_2                       12                             66
  CLUS_3                       17                             80
D41V8, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        6                             30
  CLUS_2                       40                            101
  CLUS_3                       15                             77
D41V9, multiclass
D41V10, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        4                             10
  CLUS_2                       43                            102
  CLUS_3                       14                             95
D41V11, multiclass
D41V12, multiclass
        clus
vv       DEL PEAK 21(14Q24.3) CNV DEL PEAK 21(14Q24.3) WILD-TYPE
  CLUS_1                        9                             33
  CLUS_2                       35                             70
  CLUS_3                       17                            104

Clustering(42) Variable = Del Peak 22(17q25.3)
D42V1, 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" 
D42V2, 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" 
D42V3, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        6                             46
  CLUS_2                        1                             56
  CLUS_3                        8                             46
  CLUS_4                        2                            104
D42V4, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                       10                            112
  CLUS_2                        4                             38
  CLUS_3                        1                             65
  CLUS_4                        2                             32
D42V5, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        2                             50
  CLUS_2                        3                             59
  CLUS_3                        8                             60
  CLUS_4                        3                             71
D42V6, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        0                              8
  CLUS_2                       12                            117
  CLUS_3                        4                            115
D42V7, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        7                             87
  CLUS_2                        5                             73
  CLUS_3                        5                             92
D42V8, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        1                             35
  CLUS_2                       13                            128
  CLUS_3                        3                             89
D42V9, multiclass
D42V10, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        2                             12
  CLUS_2                       11                            134
  CLUS_3                        4                            105
D42V11, multiclass
D42V12, multiclass
        clus
vv       DEL PEAK 22(17Q25.3) CNV DEL PEAK 22(17Q25.3) WILD-TYPE
  CLUS_1                        4                             38
  CLUS_2                        8                             97
  CLUS_3                        5                            116

Clustering(43) Variable = Del Peak 23(18p11.32)
D43V1, 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
D43V2, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         1                               6
  CLUS_2                         0                               6
  CLUS_3                         2                               8
  CLUS_4                         2                               2
D43V3, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         8                              44
  CLUS_2                         7                              50
  CLUS_3                        15                              39
  CLUS_4                        12                              94
D43V4, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                        22                             100
  CLUS_2                         7                              35
  CLUS_3                        12                              54
  CLUS_4                         1                              33
D43V5, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         5                              47
  CLUS_2                        11                              51
  CLUS_3                        14                              54
  CLUS_4                        12                              62
D43V6, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         3                               5
  CLUS_2                        25                             104
  CLUS_3                        14                             105
D43V7, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                        15                              79
  CLUS_2                        12                              66
  CLUS_3                        15                              82
D43V8, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         5                              31
  CLUS_2                        22                             119
  CLUS_3                        15                              77
D43V9, multiclass
D43V10, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         2                              12
  CLUS_2                        25                             120
  CLUS_3                        15                              94
D43V11, multiclass
D43V12, multiclass
        clus
vv       DEL PEAK 23(18P11.32) CNV DEL PEAK 23(18P11.32) WILD-TYPE
  CLUS_1                         6                              36
  CLUS_2                        19                              86
  CLUS_3                        17                             104

Clustering(44) Variable = Del Peak 24(18q23)
D44V1, 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
D44V2, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      1                            6
  CLUS_2                      0                            6
  CLUS_3                      2                            8
  CLUS_4                      2                            2
D44V3, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      6                           46
  CLUS_2                      6                           51
  CLUS_3                     14                           40
  CLUS_4                     17                           89
D44V4, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                     20                          102
  CLUS_2                      7                           35
  CLUS_3                     15                           51
  CLUS_4                      1                           33
D44V5, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      6                           46
  CLUS_2                     13                           49
  CLUS_3                     13                           55
  CLUS_4                     10                           64
D44V6, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      2                            6
  CLUS_2                     26                          103
  CLUS_3                     14                          105
D44V7, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                     12                           82
  CLUS_2                     16                           62
  CLUS_3                     15                           82
D44V8, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      7                           29
  CLUS_2                     22                          119
  CLUS_3                     14                           78
D44V9, multiclass
D44V10, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      3                           11
  CLUS_2                     26                          119
  CLUS_3                     14                           95
D44V11, multiclass
D44V12, multiclass
        clus
vv       DEL PEAK 24(18Q23) CNV DEL PEAK 24(18Q23) WILD-TYPE
  CLUS_1                      5                           37
  CLUS_2                     22                           83
  CLUS_3                     16                          105

Clustering(45) Variable = Del Peak 25(19q13.42)
D45V1, 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
D45V2, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         7                               0
  CLUS_2                         3                               3
  CLUS_3                         7                               3
  CLUS_4                         4                               0
D45V3, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        13                              39
  CLUS_2                         9                              48
  CLUS_3                        39                              15
  CLUS_4                        75                              31
D45V4, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        53                              69
  CLUS_2                         4                              38
  CLUS_3                        66                               0
  CLUS_4                        10                              24
D45V5, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        17                              35
  CLUS_2                        29                              33
  CLUS_3                        40                              28
  CLUS_4                        48                              26
D45V6, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         5                               3
  CLUS_2                        64                              65
  CLUS_3                        65                              54
D45V7, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        27                              67
  CLUS_2                        50                              28
  CLUS_3                        59                              38
D45V8, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                        36                               0
  CLUS_2                        47                              94
  CLUS_3                        53                              39
D45V9, multiclass
D45V10, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         1                              13
  CLUS_2                        69                              76
  CLUS_3                        66                              43
D45V11, multiclass
D45V12, multiclass
        clus
vv       DEL PEAK 25(19Q13.42) CNV DEL PEAK 25(19Q13.42) WILD-TYPE
  CLUS_1                         5                              37
  CLUS_2                        57                              48
  CLUS_3                        74                              47

Clustering(46) Variable = Del Peak 26(22q13.31)
D46V1, 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
D46V2, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         0                               7
  CLUS_2                         0                               6
  CLUS_3                         4                               6
  CLUS_4                         2                               2
D46V3, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                        11                              41
  CLUS_2                        14                              43
  CLUS_3                        15                              39
  CLUS_4                         0                             106
D46V4, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                        23                              99
  CLUS_2                        13                              29
  CLUS_3                         0                              66
  CLUS_4                         3                              31
D46V5, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         4                              48
  CLUS_2                        22                              40
  CLUS_3                         8                              60
  CLUS_4                         6                              68
D46V6, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         1                               7
  CLUS_2                        28                             101
  CLUS_3                        11                             108
D46V7, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                        28                              66
  CLUS_2                         5                              73
  CLUS_3                         7                              90
D46V8, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         0                              36
  CLUS_2                        33                             108
  CLUS_3                         7                              85
D46V9, multiclass
D46V10, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                         3                              11
  CLUS_2                        28                             117
  CLUS_3                         9                             100
D46V11, multiclass
D46V12, multiclass
        clus
vv       DEL PEAK 26(22Q13.31) CNV DEL PEAK 26(22Q13.31) WILD-TYPE
  CLUS_1                        11                              31
  CLUS_2                        19                              86
  CLUS_3                        10                             111

Clustering(47) Variable = Del Peak 27(Xp22.2)
D47V1, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                       1                             8
  CLUS_2                       2                             8
  CLUS_3                       2                             6
D47V2, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       2                             4
  CLUS_3                       1                             9
  CLUS_4                       2                             2
D47V3, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                      14                            38
  CLUS_2                       5                            52
  CLUS_3                      28                            26
  CLUS_4                      11                            95
D47V4, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                      32                            90
  CLUS_2                       7                            35
  CLUS_3                      16                            50
  CLUS_4                       3                            31
D47V5, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                       7                            45
  CLUS_2                      20                            42
  CLUS_3                      18                            50
  CLUS_4                      12                            62
D47V6, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      37                            92
  CLUS_3                      18                           101
D47V7, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                      21                            73
  CLUS_2                      17                            61
  CLUS_3                      20                            77
D47V8, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                      12                            24
  CLUS_2                      32                           109
  CLUS_3                      14                            78
D47V9, multiclass
D47V10, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                       1                            13
  CLUS_2                      38                           107
  CLUS_3                      19                            90
D47V11, multiclass
D47V12, multiclass
        clus
vv       DEL PEAK 27(XP22.2) CNV DEL PEAK 27(XP22.2) WILD-TYPE
  CLUS_1                       6                            36
  CLUS_2                      31                            74
  CLUS_3                      21                           100

Clustering(48) Variable = Del Peak 28(Xq21.1)
D48V1, 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
D48V2, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       0                             7
  CLUS_2                       1                             5
  CLUS_3                       1                             9
  CLUS_4                       4                             0
D48V3, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       6                            46
  CLUS_2                       3                            54
  CLUS_3                      18                            36
  CLUS_4                       8                            98
D48V4, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                      15                           107
  CLUS_2                       6                            36
  CLUS_3                      13                            53
  CLUS_4                       1                            33
D48V5, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       7                            45
  CLUS_2                      15                            47
  CLUS_3                       7                            61
  CLUS_4                       5                            69
D48V6, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       2                             6
  CLUS_2                      22                           107
  CLUS_3                      10                           109
D48V7, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                      15                            79
  CLUS_2                      10                            68
  CLUS_3                      10                            87
D48V8, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                      10                            26
  CLUS_2                      18                           123
  CLUS_3                       7                            85
D48V9, multiclass
D48V10, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       3                            11
  CLUS_2                      22                           123
  CLUS_3                      10                            99
D48V11, multiclass
D48V12, multiclass
        clus
vv       DEL PEAK 28(XQ21.1) CNV DEL PEAK 28(XQ21.1) WILD-TYPE
  CLUS_1                       5                            37
  CLUS_2                      15                            90
  CLUS_3                      15                           106
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
