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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/376223/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP-TP/2909316/1.GDAC_mergedClustering.Finished/KIRP-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-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=KIRP-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=127, in cluster file=127, common to both=127
[1] "Reduce the number of clustering variables from 34 to 33."
[1]  33 127
[1] "Amp Peak 1(2q32.1) mutation analysis"
[1] 3
  AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE 
                          23                          104 
  AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE 
                          23                          104 
[1] "Amp Peak 2(3p14.1) mutation analysis"
[1] 3
  AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE 
                          32                           95 
  AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE 
                          32                           95 
[1] "Amp Peak 3(3q26.31) mutation analysis"
[1] 3
  AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE 
                           42                            85 
  AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE 
                           42                            85 
[1] "Amp Peak 4(5q35.2) mutation analysis"
[1] 3
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          19                          108 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          19                          108 
[1] "Amp Peak 5(6p12.3) mutation analysis"
[1] 3
  AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE 
                           4                          123 
  AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE 
                           4                          123 
[1] "Amp Peak 6(7q22.1) mutation analysis"
[1] 3
  AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE 
                          71                           56 
  AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE 
                          71                           56 
[1] "Amp Peak 7(17q25.2) mutation analysis"
[1] 3
  AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE 
                           87                            40 
  AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE 
                           87                            40 
[1] "Amp Peak 8(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE 
                           14                           113 
  AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE 
                           14                           113 
[1] "Amp Peak 9(19q13.11) mutation analysis"
[1] 3
  AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE 
                             4                            123 
  AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE 
                             4                            123 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            27                            100 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            27                            100 
[1] "Del Peak  2(2p11.2) mutation analysis"
[1] 3
  DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE 
                            3                           124 
  DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE 
                            3                           124 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            5                           122 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            5                           122 
[1] "Del Peak  4(3p22.1) mutation analysis"
[1] 3
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                           10                           117 
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                           10                           117 
[1] "Del Peak  5(4q33) mutation analysis"
[1] 3
  DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE 
                         16                         111 
  DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE 
                         16                         111 
[1] "Del Peak  6(5p15.2) mutation analysis"
[1] 3
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                            7                           120 
  DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE 
                            7                           120 
[1] "Del Peak  7(5q15) mutation analysis"
[1] 3
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                         10                         117 
  DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE 
                         10                         117 
[1] "Del Peak  8(5q35.2) mutation analysis"
[1] 3
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            9                           118 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            9                           118 
[1] "Del Peak  9(6p12.3) mutation analysis"
[1] 3
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           12                           115 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           12                           115 
[1] "Del Peak 10(6q22.31) mutation analysis"
[1] 3
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            14                            113 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            14                            113 
[1] "Del Peak 11(6q26) mutation analysis"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         15                         112 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         15                         112 
[1] "Del Peak 12(9p21.3) mutation analysis"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           19                           108 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           19                           108 
[1] "Del Peak 13(10p15.3) mutation analysis"
[1] 3
  DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE 
                             8                            119 
  DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE 
                             8                            119 
[1] "Del Peak 14(11q22.3) mutation analysis"
[1] 3
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            14                            113 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            14                            113 
[1] "Del Peak 16(14q11.2) mutation analysis"
[1] 3
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            29                             98 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            29                             98 
[1] "Del Peak 17(14q23.3) mutation analysis"
[1] 3
  DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE 
                            28                             99 
  DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE 
                            28                             99 
[1] "Del Peak 18(14q32.2) mutation analysis"
[1] 3
  DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE 
                            28                             99 
  DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE 
                            28                             99 
[1] "Del Peak 19(15q14) mutation analysis"
[1] 3
  DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE 
                          16                          111 
  DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE 
                          16                          111 
[1] "Del Peak 20(19p13.3) mutation analysis"
[1] 3
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            13                            114 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            13                            114 
[1] "Del Peak 21(19q13.2) mutation analysis"
[1] 3
  DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE 
                            11                            116 
  DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE 
                            11                            116 
[1] "Del Peak 22(19q13.42) mutation analysis"
[1] 3
  DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE 
                             12                             115 
  DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE 
                             12                             115 
[1] "Del Peak 23(22q12.2) mutation analysis"
[1] 3
  DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE 
                            34                             93 
  DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE 
                            34                             93 
[1] "Del Peak 24(Xq21.31) mutation analysis"
[1] 3
  DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE 
                            18                            109 
  DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE 
                            18                            109 
[1] "Del Peak 25(Xq28) mutation analysis"
[1] 3
  DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE 
                         17                         110 
  DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE 
                         17                         110 
[1] "data2feature, selection=ALL"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 127 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 127 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(2q32.1) mutation analysis
D1V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2Q32.1) MUTATED      2    1
  AMP PEAK 1(2Q32.1) WILD-TYPE    5    8
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          2                            5
  CLUS_2                          1                            8
D1V2, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          0                            4
  CLUS_2                          2                            5
  CLUS_3                          1                            4
D1V3, multiclass
D1V4, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          2                           25
  CLUS_2                          9                           44
  CLUS_3                          9                           22
D1V5, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          6                           21
  CLUS_2                          6                           18
  CLUS_3                          5                           20
D1V6, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          4                           14
  CLUS_2                          8                           29
  CLUS_3                          5                           16
D1V7, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          5                           22
  CLUS_2                          6                           32
  CLUS_3                          5                           30
  CLUS_4                          4                           13
D1V8, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          5                           22
  CLUS_2                          6                           39
  CLUS_3                          4                            8
  CLUS_4                          5                           28

Clustering(2) Variable = Amp Peak 2(3p14.1) mutation analysis
D2V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(3P14.1) MUTATED      3    3
  AMP PEAK 2(3P14.1) WILD-TYPE    4    6
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          3                            4
  CLUS_2                          3                            6
D2V2, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          1                            3
  CLUS_2                          2                            5
  CLUS_3                          3                            2
D2V3, multiclass
D2V4, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          5                           22
  CLUS_2                         18                           35
  CLUS_3                          3                           28
D2V5, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                         12                           15
  CLUS_2                          1                           23
  CLUS_3                          7                           18
D2V6, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          1                           17
  CLUS_2                         19                           18
  CLUS_3                          0                           21
D2V7, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          8                           19
  CLUS_2                          6                           32
  CLUS_3                         16                           19
  CLUS_4                          1                           16
D2V8, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          2                           25
  CLUS_2                          8                           37
  CLUS_3                          8                            4
  CLUS_4                         13                           20

Clustering(3) Variable = Amp Peak 3(3q26.31) mutation analysis
D3V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(3Q26.31) MUTATED      4    2
  AMP PEAK 3(3Q26.31) WILD-TYPE    3    7
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                           4                             3
  CLUS_2                           2                             7
D3V2, multiclass
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           2                             5
  CLUS_3                           4                             1
D3V3, multiclass
D3V4, multiclass
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                           6                            21
  CLUS_2                          22                            31
  CLUS_3                           8                            23
D3V5, multiclass
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                          14                            13
  CLUS_2                           4                            20
  CLUS_3                           8                            17
D3V6, multiclass
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                          20                            17
  CLUS_3                           2                            19
D3V7, multiclass
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                          11                            16
  CLUS_2                           8                            30
  CLUS_3                          16                            19
  CLUS_4                           3                            14
D3V8, multiclass
        clus
vv       AMP PEAK 3(3Q26.31) MUTATED AMP PEAK 3(3Q26.31) WILD-TYPE
  CLUS_1                           5                            22
  CLUS_2                          10                            35
  CLUS_3                           9                             3
  CLUS_4                          14                            19

Clustering(4) Variable = Amp Peak 4(5q35.2) mutation analysis
D4V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      3    0
  AMP PEAK 4(5Q35.2) WILD-TYPE    4    9
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          3                            4
  CLUS_2                          0                            9
D4V2, multiclass
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          0                            4
  CLUS_2                          3                            4
  CLUS_3                          0                            5
D4V3, multiclass
D4V4, multiclass
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          5                           22
  CLUS_2                          3                           50
  CLUS_3                          8                           23
D4V5, multiclass
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          3                           24
  CLUS_2                          4                           20
  CLUS_3                          5                           20
D4V6, multiclass
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          1                           17
  CLUS_2                          4                           33
  CLUS_3                          7                           14
D4V7, multiclass
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          5                           22
  CLUS_2                          4                           34
  CLUS_3                          3                           32
  CLUS_4                          3                           14
D4V8, multiclass
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  CLUS_1                          8                           19
  CLUS_2                          3                           42
  CLUS_3                          1                           11
  CLUS_4                          3                           30

Clustering(5) Variable = Amp Peak 5(6p12.3) mutation analysis
D5V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(6P12.3) MUTATED      0    0
  AMP PEAK 5(6P12.3) WILD-TYPE    7    9
D5V2, multiclass
D5V3, multiclass
D5V4, multiclass
        clus
vv       AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE
  CLUS_1                          0                           27
  CLUS_2                          1                           52
  CLUS_3                          3                           28
D5V5, multiclass
        clus
vv       AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE
  CLUS_1                          1                           26
  CLUS_2                          3                           21
  CLUS_3                          0                           25
D5V6, multiclass
        clus
vv       AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE
  CLUS_1                          2                           16
  CLUS_2                          1                           36
  CLUS_3                          1                           20
D5V7, multiclass
        clus
vv       AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE
  CLUS_1                          0                           27
  CLUS_2                          3                           35
  CLUS_3                          0                           35
  CLUS_4                          1                           16
D5V8, multiclass
        clus
vv       AMP PEAK 5(6P12.3) MUTATED AMP PEAK 5(6P12.3) WILD-TYPE
  CLUS_1                          0                           27
  CLUS_2                          3                           42
  CLUS_3                          1                           11
  CLUS_4                          0                           33

Clustering(6) Variable = Amp Peak 6(7q22.1) mutation analysis
D6V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 6(7Q22.1) MUTATED      5    6
  AMP PEAK 6(7Q22.1) WILD-TYPE    2    3
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                          5                            2
  CLUS_2                          6                            3
D6V2, multiclass
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                          3                            1
  CLUS_2                          4                            3
  CLUS_3                          4                            1
D6V3, multiclass
D6V4, multiclass
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                         10                           17
  CLUS_2                         40                           13
  CLUS_3                         10                           21
D6V5, multiclass
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                         22                            5
  CLUS_2                          8                           16
  CLUS_3                         13                           12
D6V6, multiclass
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                          8                           10
  CLUS_2                         29                            8
  CLUS_3                          6                           15
D6V7, multiclass
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                         12                           15
  CLUS_2                         20                           18
  CLUS_3                         28                            7
  CLUS_4                          8                            9
D6V8, multiclass
        clus
vv       AMP PEAK 6(7Q22.1) MUTATED AMP PEAK 6(7Q22.1) WILD-TYPE
  CLUS_1                         11                           16
  CLUS_2                         23                           22
  CLUS_3                         10                            2
  CLUS_4                         24                            9

Clustering(7) Variable = Amp Peak 7(17q25.2) mutation analysis
D7V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.2) MUTATED      6    6
  AMP PEAK 7(17Q25.2) WILD-TYPE    1    3
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                           6                             1
  CLUS_2                           6                             3
D7V2, multiclass
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                           3                             1
  CLUS_2                           5                             2
  CLUS_3                           4                             1
D7V3, multiclass
D7V4, multiclass
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                          15                            12
  CLUS_2                          41                            12
  CLUS_3                          19                            12
D7V5, multiclass
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                          20                             7
  CLUS_2                          13                            11
  CLUS_3                          14                            11
D7V6, multiclass
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                          10                             8
  CLUS_2                          28                             9
  CLUS_3                           9                            12
D7V7, multiclass
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                          19                             8
  CLUS_2                          26                            12
  CLUS_3                          25                            10
  CLUS_4                          10                             7
D7V8, multiclass
        clus
vv       AMP PEAK 7(17Q25.2) MUTATED AMP PEAK 7(17Q25.2) WILD-TYPE
  CLUS_1                          16                            11
  CLUS_2                          30                            15
  CLUS_3                          10                             2
  CLUS_4                          24                             9

Clustering(8) Variable = Amp Peak 8(19p13.2) mutation analysis
D8V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 8(19P13.2) MUTATED      0    4
  AMP PEAK 8(19P13.2) WILD-TYPE    7    5
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           4                             5
D8V2, multiclass
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           1                             6
  CLUS_3                           1                             4
D8V3, multiclass
D8V4, multiclass
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           7                            46
  CLUS_3                           3                            28
D8V5, multiclass
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           7                            20
  CLUS_2                           3                            21
  CLUS_3                           1                            24
D8V6, multiclass
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           3                            15
  CLUS_2                           6                            31
  CLUS_3                           2                            19
D8V7, multiclass
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           4                            34
  CLUS_3                           5                            30
  CLUS_4                           3                            14
D8V8, multiclass
        clus
vv       AMP PEAK 8(19P13.2) MUTATED AMP PEAK 8(19P13.2) WILD-TYPE
  CLUS_1                           3                            24
  CLUS_2                           4                            41
  CLUS_3                           1                            11
  CLUS_4                           6                            27

Clustering(9) Variable = Amp Peak 9(19q13.11) mutation analysis
D9V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 9(19Q13.11) MUTATED      0    0
  AMP PEAK 9(19Q13.11) WILD-TYPE    7    9
D9V2, multiclass
D9V3, multiclass
D9V4, multiclass
        clus
vv       AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE
  CLUS_1                            0                             27
  CLUS_2                            1                             52
  CLUS_3                            3                             28
D9V5, multiclass
        clus
vv       AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE
  CLUS_1                            0                             27
  CLUS_2                            2                             22
  CLUS_3                            1                             24
D9V6, multiclass
        clus
vv       AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE
  CLUS_1                            1                             17
  CLUS_2                            0                             37
  CLUS_3                            2                             19
D9V7, multiclass
        clus
vv       AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            3                             35
  CLUS_3                            0                             35
  CLUS_4                            0                             17
D9V8, multiclass
        clus
vv       AMP PEAK 9(19Q13.11) MUTATED AMP PEAK 9(19Q13.11) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            3                             42
  CLUS_3                            0                             12
  CLUS_4                            0                             33

Clustering(10) Variable = Del Peak  1(1p36.31) mutation analysis
D10V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1    2
  DEL PEAK  1(1P36.31) WILD-TYPE    6    7
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            2                              7
D10V2, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            2                              5
  CLUS_3                            1                              4
D10V3, multiclass
D10V4, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            7                             46
  CLUS_3                           13                             18
D10V5, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            9                             15
  CLUS_3                            3                             22
D10V6, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                            4                             33
  CLUS_3                            6                             15
D10V7, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            5                             33
  CLUS_3                            9                             26
  CLUS_4                            5                             12
D10V8, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                            8                             37
  CLUS_3                            0                             12
  CLUS_4                            9                             24

Clustering(11) Variable = Del Peak  2(2p11.2) mutation analysis
D11V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P11.2) MUTATED      0    0
  DEL PEAK  2(2P11.2) WILD-TYPE    7    9
D11V2, multiclass
D11V3, multiclass
D11V4, multiclass
        clus
vv       DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           2                            51
  CLUS_3                           1                            30
D11V5, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  2(2P11.2) MUTATED"
clus
  DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE 
                            2                            74 
                   TCGA-A4-7997                    TCGA-AL-3466 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-AL-3467                    TCGA-AL-3468 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-AL-3471                    TCGA-AL-3472 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-AL-3473                    TCGA-B1-5398 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B3-3925                    TCGA-B3-3926 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B3-4103                    TCGA-B3-4104 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-4113                    TCGA-B9-4114 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-4115                    TCGA-B9-4116 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-4117                    TCGA-B9-4617 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-5156                    TCGA-BQ-5876 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5877                    TCGA-BQ-5878 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5879                    TCGA-BQ-5880 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5881                    TCGA-BQ-5882 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5883                    TCGA-BQ-5884 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5886                    TCGA-BQ-5887 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5888                    TCGA-BQ-5889 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5890                    TCGA-BQ-5891 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5892                    TCGA-BQ-5893 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5894                    TCGA-BQ-7044 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7045                    TCGA-BQ-7046 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7048                    TCGA-BQ-7049 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7050                    TCGA-BQ-7051 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7053                    TCGA-BQ-7056 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7058                    TCGA-BQ-7059 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7060                    TCGA-BQ-7061 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7062                    TCGA-DW-5560 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-DW-5561                    TCGA-DZ-6131 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-DZ-6132                    TCGA-DZ-6133 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-DZ-6134                    TCGA-DZ-6135 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-EV-5901                    TCGA-EV-5902 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-EV-5903                    TCGA-G7-6789 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6793 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-6795                    TCGA-G7-6796 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-6797                    TCGA-G7-7501 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-7502                    TCGA-GL-6846 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-GL-7966                    TCGA-HE-7128 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-HE-7129                    TCGA-HE-7130 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
D11V6, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  2(2P11.2) MUTATED"
clus
  DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE 
                            2                            74 
                   TCGA-A4-7997                    TCGA-AL-3466 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-AL-3467                    TCGA-AL-3468 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-AL-3471                    TCGA-AL-3472 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-AL-3473                    TCGA-B1-5398 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B3-3925                    TCGA-B3-3926 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B3-4103                    TCGA-B3-4104 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-4113                    TCGA-B9-4114 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-4115                    TCGA-B9-4116 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-4117                    TCGA-B9-4617 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-B9-5156                    TCGA-BQ-5876 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5877                    TCGA-BQ-5878 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5879                    TCGA-BQ-5880 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5881                    TCGA-BQ-5882 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5883                    TCGA-BQ-5884 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5886                    TCGA-BQ-5887 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5888                    TCGA-BQ-5889 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5890                    TCGA-BQ-5891 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5892                    TCGA-BQ-5893 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-5894                    TCGA-BQ-7044 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7045                    TCGA-BQ-7046 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7048                    TCGA-BQ-7049 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7050                    TCGA-BQ-7051 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7053                    TCGA-BQ-7056 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7058                    TCGA-BQ-7059 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7060                    TCGA-BQ-7061 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-BQ-7062                    TCGA-DW-5560 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-DW-5561                    TCGA-DZ-6131 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-DZ-6132                    TCGA-DZ-6133 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-DZ-6134                    TCGA-DZ-6135 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-EV-5901                    TCGA-EV-5902 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-EV-5903                    TCGA-G7-6789 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6793 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-6795                    TCGA-G7-6796 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-6797                    TCGA-G7-7501 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-G7-7502                    TCGA-GL-6846 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-GL-7966                    TCGA-HE-7128 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
                   TCGA-HE-7129                    TCGA-HE-7130 
"DEL PEAK  2(2P11.2) WILD-TYPE" "DEL PEAK  2(2P11.2) WILD-TYPE" 
D11V7, multiclass
        clus
vv       DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           0                            38
  CLUS_3                           0                            35
  CLUS_4                           2                            15
D11V8, multiclass
        clus
vv       DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE
  CLUS_1                           3                            24
  CLUS_2                           0                            45
  CLUS_3                           0                            12
  CLUS_4                           0                            33

Clustering(12) Variable = Del Peak  3(2q37.3) mutation analysis
D12V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      1    1
  DEL PEAK  3(2Q37.3) WILD-TYPE    6    8
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           1                             8
D12V2, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  3(2Q37.3) MUTATED"
clus
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            2                            14 
                   TCGA-AL-3466                    TCGA-AL-3467 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-AL-3468                    TCGA-AL-3471 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-AL-3472                    TCGA-AL-3473 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-B3-3925                    TCGA-B3-3926 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-B3-4103                    TCGA-B9-4113 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-B9-4114                    TCGA-B9-4115 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-B9-4116                    TCGA-B9-4617 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
D12V3, multiclass
D12V4, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           0                            53
  CLUS_3                           2                            29
D12V5, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           2                            22
  CLUS_3                           1                            24
D12V6, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           2                            16
  CLUS_2                           1                            36
  CLUS_3                           1                            20
D12V7, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           1                            37
  CLUS_3                           1                            34
  CLUS_4                           1                            16
D12V8, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           2                            43
  CLUS_3                           0                            12
  CLUS_4                           1                            32

Clustering(13) Variable = Del Peak  4(3p22.1) mutation analysis
D13V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P22.1) MUTATED      1    0
  DEL PEAK  4(3P22.1) WILD-TYPE    6    9
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           0                             9
D13V2, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  4(3P22.1) MUTATED"
clus
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                            1                            15 
                   TCGA-AL-3466                    TCGA-AL-3467 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-AL-3468                    TCGA-AL-3471 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-AL-3472                    TCGA-B3-3925 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-B3-3926                    TCGA-B3-4103 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-B3-4104                    TCGA-B9-4113 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-B9-4114                    TCGA-B9-4115 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-B9-4116                    TCGA-B9-4117 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-B9-4617 
"DEL PEAK  4(3P22.1) WILD-TYPE" 
D13V3, multiclass
D13V4, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           0                            53
  CLUS_3                           8                            23
D13V5, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           5                            19
  CLUS_3                           2                            23
D13V6, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           2                            16
  CLUS_2                           0                            37
  CLUS_3                           5                            16
D13V7, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           2                            36
  CLUS_3                           0                            35
  CLUS_4                           4                            13
D13V8, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           4                            23
  CLUS_2                           3                            42
  CLUS_3                           1                            11
  CLUS_4                           0                            33

Clustering(14) Variable = Del Peak  5(4q33) mutation analysis
D14V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q33) MUTATED      1    2
  DEL PEAK  5(4Q33) WILD-TYPE    6    7
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         1                           6
  CLUS_2                         2                           7
D14V2, multiclass
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         0                           4
  CLUS_2                         2                           5
  CLUS_3                         1                           4
D14V3, multiclass
D14V4, multiclass
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         2                          25
  CLUS_2                         1                          52
  CLUS_3                        10                          21
D14V5, multiclass
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         1                          26
  CLUS_2                         8                          16
  CLUS_3                         1                          24
D14V6, multiclass
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         4                          14
  CLUS_2                         1                          36
  CLUS_3                         5                          16
D14V7, multiclass
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          31
  CLUS_3                         2                          33
  CLUS_4                         2                          15
D14V8, multiclass
        clus
vv       DEL PEAK  5(4Q33) MUTATED DEL PEAK  5(4Q33) WILD-TYPE
  CLUS_1                         4                          23
  CLUS_2                         6                          39
  CLUS_3                         2                          10
  CLUS_4                         2                          31

Clustering(15) Variable = Del Peak  6(5p15.2) mutation analysis
D15V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5P15.2) MUTATED      0    0
  DEL PEAK  6(5P15.2) WILD-TYPE    7    9
D15V2, multiclass
D15V3, multiclass
D15V4, multiclass
        clus
vv       DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           1                            52
  CLUS_3                           5                            26
D15V5, multiclass
        clus
vv       DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           4                            20
  CLUS_3                           0                            25
D15V6, multiclass
        clus
vv       DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                           1                            36
  CLUS_3                           0                            21
D15V7, multiclass
        clus
vv       DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           4                            34
  CLUS_3                           1                            34
  CLUS_4                           0                            17
D15V8, multiclass
        clus
vv       DEL PEAK  6(5P15.2) MUTATED DEL PEAK  6(5P15.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           4                            41
  CLUS_3                           0                            12
  CLUS_4                           2                            31

Clustering(16) Variable = Del Peak  7(5q15) mutation analysis
D16V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(5Q15) MUTATED      0    0
  DEL PEAK  7(5Q15) WILD-TYPE    7    9
D16V2, multiclass
D16V3, multiclass
D16V4, multiclass
        clus
vv       DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  CLUS_1                         2                          25
  CLUS_2                         2                          51
  CLUS_3                         6                          25
D16V5, multiclass
        clus
vv       DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  CLUS_1                         1                          26
  CLUS_2                         5                          19
  CLUS_3                         0                          25
D16V6, multiclass
        clus
vv       DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  CLUS_1                         4                          14
  CLUS_2                         1                          36
  CLUS_3                         1                          20
D16V7, multiclass
        clus
vv       DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  CLUS_1                         2                          25
  CLUS_2                         4                          34
  CLUS_3                         2                          33
  CLUS_4                         1                          16
D16V8, multiclass
        clus
vv       DEL PEAK  7(5Q15) MUTATED DEL PEAK  7(5Q15) WILD-TYPE
  CLUS_1                         1                          26
  CLUS_2                         6                          39
  CLUS_3                         1                          11
  CLUS_4                         1                          32

Clustering(17) Variable = Del Peak  8(5q35.2) mutation analysis
D17V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      0    1
  DEL PEAK  8(5Q35.2) WILD-TYPE    7    8
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           1                             8
D17V2, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  8(5Q35.2) MUTATED"
clus
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            1                            15 
                   TCGA-AL-3466                    TCGA-AL-3467 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-AL-3468                    TCGA-AL-3471 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-AL-3472                    TCGA-AL-3473 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-B3-3925                    TCGA-B3-3926 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-B3-4103                    TCGA-B9-4113 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-B9-4114                    TCGA-B9-4115 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-B9-4116                    TCGA-B9-4117 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-B9-4617 
"DEL PEAK  8(5Q35.2) WILD-TYPE" 
D17V3, multiclass
D17V4, multiclass
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           0                            53
  CLUS_3                           6                            25
D17V5, multiclass
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           6                            18
  CLUS_3                           0                            25
D17V6, multiclass
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           0                            37
  CLUS_3                           1                            20
D17V7, multiclass
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           5                            33
  CLUS_3                           1                            34
  CLUS_4                           1                            16
D17V8, multiclass
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           6                            39
  CLUS_3                           1                            11
  CLUS_4                           1                            32

Clustering(18) Variable = Del Peak  9(6p12.3) mutation analysis
D18V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      0    1
  DEL PEAK  9(6P12.3) WILD-TYPE    7    8
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           1                             8
D18V2, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  9(6P12.3) MUTATED"
clus
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                            1                            15 
                   TCGA-AL-3466                    TCGA-AL-3467 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-AL-3468                    TCGA-AL-3471 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-AL-3472                    TCGA-AL-3473 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-B3-3925                    TCGA-B3-4103 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-B3-4104                    TCGA-B9-4113 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-B9-4114                    TCGA-B9-4115 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-B9-4116                    TCGA-B9-4117 
"DEL PEAK  9(6P12.3) WILD-TYPE" "DEL PEAK  9(6P12.3) WILD-TYPE" 
                   TCGA-B9-4617 
"DEL PEAK  9(6P12.3) WILD-TYPE" 
D18V3, multiclass
D18V4, multiclass
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           3                            50
  CLUS_3                           7                            24
D18V5, multiclass
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  CLUS_1                           4                            23
  CLUS_2                           4                            20
  CLUS_3                           2                            23
D18V6, multiclass
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  CLUS_1                           2                            16
  CLUS_2                           4                            33
  CLUS_3                           4                            17
D18V7, multiclass
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  CLUS_1                           3                            24
  CLUS_2                           3                            35
  CLUS_3                           5                            30
  CLUS_4                           0                            17
D18V8, multiclass
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           5                            40
  CLUS_3                           0                            12
  CLUS_4                           4                            29

Clustering(19) Variable = Del Peak 10(6q22.31) mutation analysis
D19V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED      0    1
  DEL PEAK 10(6Q22.31) WILD-TYPE    7    8
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  CLUS_1                            0                              7
  CLUS_2                            1                              8
D19V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 10(6Q22.31) MUTATED"
clus
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             1                             15 
                    TCGA-AL-3466                     TCGA-AL-3467 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-AL-3468                     TCGA-AL-3471 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-AL-3472                     TCGA-AL-3473 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-B3-3925                     TCGA-B3-4103 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-B3-4104                     TCGA-B9-4113 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-B9-4114                     TCGA-B9-4115 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-B9-4116                     TCGA-B9-4117 
"DEL PEAK 10(6Q22.31) WILD-TYPE" "DEL PEAK 10(6Q22.31) WILD-TYPE" 
                    TCGA-B9-4617 
"DEL PEAK 10(6Q22.31) WILD-TYPE" 
D19V3, multiclass
D19V4, multiclass
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            2                             51
  CLUS_3                            7                             24
D19V5, multiclass
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            6                             18
  CLUS_3                            1                             24
D19V6, multiclass
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            3                             34
  CLUS_3                            2                             19
D19V7, multiclass
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            5                             33
  CLUS_3                            5                             30
  CLUS_4                            1                             16
D19V8, multiclass
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            8                             37
  CLUS_3                            0                             12
  CLUS_4                            3                             30

Clustering(20) Variable = Del Peak 11(6q26) mutation analysis
D20V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED      0    1
  DEL PEAK 11(6Q26) WILD-TYPE    7    8
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  CLUS_1                         0                           7
  CLUS_2                         1                           8
D20V2, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 11(6Q26) MUTATED"
clus
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                          1                          15 
                 TCGA-AL-3466                  TCGA-AL-3467 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-AL-3468                  TCGA-AL-3471 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-AL-3472                  TCGA-AL-3473 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-B3-3925                  TCGA-B3-4103 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-B3-4104                  TCGA-B9-4113 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-B9-4114                  TCGA-B9-4115 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-B9-4116                  TCGA-B9-4117 
"DEL PEAK 11(6Q26) WILD-TYPE" "DEL PEAK 11(6Q26) WILD-TYPE" 
                 TCGA-B9-4617 
"DEL PEAK 11(6Q26) WILD-TYPE" 
D20V3, multiclass
D20V4, multiclass
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         2                          51
  CLUS_3                         9                          22
D20V5, multiclass
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         5                          19
  CLUS_3                         2                          23
D20V6, multiclass
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  CLUS_1                         4                          14
  CLUS_2                         3                          34
  CLUS_3                         3                          18
D20V7, multiclass
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         4                          34
  CLUS_3                         5                          30
  CLUS_4                         1                          16
D20V8, multiclass
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          38
  CLUS_3                         0                          12
  CLUS_4                         3                          30

Clustering(21) Variable = Del Peak 12(9p21.3) mutation analysis
D21V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      1    2
  DEL PEAK 12(9P21.3) WILD-TYPE    6    7
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           2                             7
D21V2, multiclass
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           2                             5
  CLUS_3                           1                             4
D21V3, multiclass
D21V4, multiclass
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           6                            21
  CLUS_2                           0                            53
  CLUS_3                          10                            21
D21V5, multiclass
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                          12                            12
  CLUS_3                           2                            23
D21V6, multiclass
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           8                            10
  CLUS_2                           2                            35
  CLUS_3                           5                            16
D21V7, multiclass
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                          10                            28
  CLUS_3                           3                            32
  CLUS_4                           4                            13
D21V8, multiclass
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                          12                            33
  CLUS_3                           1                            11
  CLUS_4                           3                            30

Clustering(22) Variable = Del Peak 13(10p15.3) mutation analysis
D22V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10P15.3) MUTATED      0    0
  DEL PEAK 13(10P15.3) WILD-TYPE    7    9
D22V2, multiclass
D22V3, multiclass
D22V4, multiclass
        clus
vv       DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE
  CLUS_1                            0                             27
  CLUS_2                            2                             51
  CLUS_3                            6                             25
D22V5, multiclass
        clus
vv       DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            3                             21
  CLUS_3                            1                             24
D22V6, multiclass
        clus
vv       DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE
  CLUS_1                            1                             17
  CLUS_2                            1                             36
  CLUS_3                            3                             18
D22V7, multiclass
        clus
vv       DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE
  CLUS_1                            0                             27
  CLUS_2                            2                             36
  CLUS_3                            1                             34
  CLUS_4                            2                             15
D22V8, multiclass
        clus
vv       DEL PEAK 13(10P15.3) MUTATED DEL PEAK 13(10P15.3) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            2                             43
  CLUS_3                            2                             10
  CLUS_4                            0                             33

Clustering(23) Variable = Del Peak 14(11q22.3) mutation analysis
D23V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      0    1
  DEL PEAK 14(11Q22.3) WILD-TYPE    7    8
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  CLUS_1                            0                              7
  CLUS_2                            1                              8
D23V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 14(11Q22.3) MUTATED"
clus
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                             1                             15 
                    TCGA-AL-3466                     TCGA-AL-3467 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-AL-3468                     TCGA-AL-3471 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-AL-3472                     TCGA-AL-3473 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-B3-3925                     TCGA-B3-3926 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-B3-4103                     TCGA-B9-4113 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-B9-4114                     TCGA-B9-4115 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-B9-4116                     TCGA-B9-4117 
"DEL PEAK 14(11Q22.3) WILD-TYPE" "DEL PEAK 14(11Q22.3) WILD-TYPE" 
                    TCGA-B9-4617 
"DEL PEAK 14(11Q22.3) WILD-TYPE" 
D23V3, multiclass
D23V4, multiclass
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            2                             51
  CLUS_3                            9                             22
D23V5, multiclass
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            6                             18
  CLUS_3                            3                             22
D23V6, multiclass
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            1                             36
  CLUS_3                            4                             17
D23V7, multiclass
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            5                             33
  CLUS_3                            3                             32
  CLUS_4                            1                             16
D23V8, multiclass
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            7                             38
  CLUS_3                            1                             11
  CLUS_4                            2                             31

Clustering(24) Variable = Del Peak 16(14q11.2) mutation analysis
D24V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED      3    2
  DEL PEAK 16(14Q11.2) WILD-TYPE    4    7
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            3                              4
  CLUS_2                            2                              7
D24V2, multiclass
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            4                              3
  CLUS_3                            1                              4
D24V3, multiclass
D24V4, multiclass
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                            8                             45
  CLUS_3                            9                             22
D24V5, multiclass
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                           10                             14
  CLUS_3                            4                             21
D24V6, multiclass
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            6                             31
  CLUS_3                            6                             15
D24V7, multiclass
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             29
  CLUS_3                            7                             28
  CLUS_4                            5                             12
D24V8, multiclass
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                           10                             35
  CLUS_3                            2                             10
  CLUS_4                            7                             26

Clustering(25) Variable = Del Peak 17(14q23.3) mutation analysis
D25V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q23.3) MUTATED      2    2
  DEL PEAK 17(14Q23.3) WILD-TYPE    5    7
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            2                              7
D25V2, multiclass
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            3                              4
  CLUS_3                            1                              4
D25V3, multiclass
D25V4, multiclass
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            8                             19
  CLUS_2                            7                             46
  CLUS_3                            9                             22
D25V5, multiclass
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                           10                             14
  CLUS_3                            5                             20
D25V6, multiclass
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            4                             33
  CLUS_3                            7                             14
D25V7, multiclass
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             29
  CLUS_3                            6                             29
  CLUS_4                            5                             12
D25V8, multiclass
        clus
vv       DEL PEAK 17(14Q23.3) MUTATED DEL PEAK 17(14Q23.3) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                           10                             35
  CLUS_3                            2                             10
  CLUS_4                            6                             27

Clustering(26) Variable = Del Peak 18(14q32.2) mutation analysis
D26V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q32.2) MUTATED      2    2
  DEL PEAK 18(14Q32.2) WILD-TYPE    5    7
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            2                              7
D26V2, multiclass
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            3                              4
  CLUS_3                            1                              4
D26V3, multiclass
D26V4, multiclass
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            8                             19
  CLUS_2                            8                             45
  CLUS_3                            8                             23
D26V5, multiclass
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            9                             15
  CLUS_3                            5                             20
D26V6, multiclass
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                            4                             33
  CLUS_3                            7                             14
D26V7, multiclass
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             29
  CLUS_3                            6                             29
  CLUS_4                            5                             12
D26V8, multiclass
        clus
vv       DEL PEAK 18(14Q32.2) MUTATED DEL PEAK 18(14Q32.2) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                           10                             35
  CLUS_3                            2                             10
  CLUS_4                            6                             27

Clustering(27) Variable = Del Peak 19(15q14) mutation analysis
D27V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(15Q14) MUTATED      1    1
  DEL PEAK 19(15Q14) WILD-TYPE    6    8
        clus
vv       DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE
  CLUS_1                          1                            6
  CLUS_2                          1                            8
D27V2, multiclass
[1] "Remove cluster labels:"     "DEL PEAK 19(15Q14) MUTATED"
clus
  DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE 
                           2                           14 
                  TCGA-AL-3467                   TCGA-AL-3468 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
                  TCGA-AL-3471                   TCGA-AL-3472 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
                  TCGA-AL-3473                   TCGA-B3-3925 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
                  TCGA-B3-4103                   TCGA-B3-4104 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
                  TCGA-B9-4113                   TCGA-B9-4114 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
                  TCGA-B9-4115                   TCGA-B9-4116 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
                  TCGA-B9-4117                   TCGA-B9-4617 
"DEL PEAK 19(15Q14) WILD-TYPE" "DEL PEAK 19(15Q14) WILD-TYPE" 
D27V3, multiclass
D27V4, multiclass
        clus
vv       DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE
  CLUS_1                          4                           23
  CLUS_2                          2                           51
  CLUS_3                          8                           23
D27V5, multiclass
        clus
vv       DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE
  CLUS_1                          2                           25
  CLUS_2                          7                           17
  CLUS_3                          3                           22
D27V6, multiclass
        clus
vv       DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE
  CLUS_1                          5                           13
  CLUS_2                          5                           32
  CLUS_3                          2                           19
D27V7, multiclass
        clus
vv       DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE
  CLUS_1                          3                           24
  CLUS_2                          7                           31
  CLUS_3                          4                           31
  CLUS_4                          0                           17
D27V8, multiclass
        clus
vv       DEL PEAK 19(15Q14) MUTATED DEL PEAK 19(15Q14) WILD-TYPE
  CLUS_1                          3                           24
  CLUS_2                          8                           37
  CLUS_3                          0                           12
  CLUS_4                          3                           30

Clustering(28) Variable = Del Peak 20(19p13.3) mutation analysis
D28V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      1    0
  DEL PEAK 20(19P13.3) WILD-TYPE    6    9
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            0                              9
D28V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 20(19P13.3) MUTATED"
clus
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                             1                             15 
                    TCGA-AL-3467                     TCGA-AL-3468 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-AL-3471                     TCGA-AL-3472 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-AL-3473                     TCGA-B3-3925 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B3-3926                     TCGA-B3-4103 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B3-4104                     TCGA-B9-4113 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B9-4114                     TCGA-B9-4115 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B9-4116                     TCGA-B9-4117 
"DEL PEAK 20(19P13.3) WILD-TYPE" "DEL PEAK 20(19P13.3) WILD-TYPE" 
                    TCGA-B9-4617 
"DEL PEAK 20(19P13.3) WILD-TYPE" 
D28V3, multiclass
D28V4, multiclass
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            4                             49
  CLUS_3                            6                             25
D28V5, multiclass
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            3                             21
  CLUS_3                            2                             23
D28V6, multiclass
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  CLUS_1                            1                             17
  CLUS_2                            1                             36
  CLUS_3                            4                             17
D28V7, multiclass
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            3                             35
  CLUS_3                            3                             32
  CLUS_4                            1                             16
D28V8, multiclass
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            3                             42
  CLUS_3                            1                             11
  CLUS_4                            3                             30

Clustering(29) Variable = Del Peak 21(19q13.2) mutation analysis
D29V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(19Q13.2) MUTATED      0    0
  DEL PEAK 21(19Q13.2) WILD-TYPE    7    9
D29V2, multiclass
D29V3, multiclass
D29V4, multiclass
        clus
vv       DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            4                             49
  CLUS_3                            6                             25
D29V5, multiclass
        clus
vv       DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            2                             22
  CLUS_3                            2                             23
D29V6, multiclass
        clus
vv       DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE
  CLUS_1                            0                             18
  CLUS_2                            1                             36
  CLUS_3                            4                             17
D29V7, multiclass
        clus
vv       DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            1                             37
  CLUS_3                            2                             33
  CLUS_4                            2                             15
D29V8, multiclass
        clus
vv       DEL PEAK 21(19Q13.2) MUTATED DEL PEAK 21(19Q13.2) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            2                             43
  CLUS_3                            0                             12
  CLUS_4                            3                             30

Clustering(30) Variable = Del Peak 22(19q13.42) mutation analysis
D30V1, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(19Q13.42) MUTATED      0    0
  DEL PEAK 22(19Q13.42) WILD-TYPE    7    9
D30V2, multiclass
D30V3, multiclass
D30V4, multiclass
        clus
vv       DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE
  CLUS_1                             1                              26
  CLUS_2                             6                              47
  CLUS_3                             5                              26
D30V5, multiclass
        clus
vv       DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE
  CLUS_1                             1                              26
  CLUS_2                             2                              22
  CLUS_3                             2                              23
D30V6, multiclass
        clus
vv       DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE
  CLUS_1                             0                              18
  CLUS_2                             2                              35
  CLUS_3                             3                              18
D30V7, multiclass
        clus
vv       DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE
  CLUS_1                             4                              23
  CLUS_2                             2                              36
  CLUS_3                             2                              33
  CLUS_4                             2                              15
D30V8, multiclass
        clus
vv       DEL PEAK 22(19Q13.42) MUTATED DEL PEAK 22(19Q13.42) WILD-TYPE
  CLUS_1                             4                              23
  CLUS_2                             2                              43
  CLUS_3                             1                              11
  CLUS_4                             3                              30

Clustering(31) Variable = Del Peak 23(22q12.2) mutation analysis
D31V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(22Q12.2) MUTATED      2    1
  DEL PEAK 23(22Q12.2) WILD-TYPE    5    8
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            1                              8
D31V2, multiclass
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            2                              5
  CLUS_3                            1                              4
D31V3, multiclass
D31V4, multiclass
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             44
  CLUS_3                           17                             14
D31V5, multiclass
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                            6                             21
  CLUS_2                            9                             15
  CLUS_3                            8                             17
D31V6, multiclass
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            7                             30
  CLUS_3                           11                             10
D31V7, multiclass
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                            6                             21
  CLUS_2                            7                             31
  CLUS_3                            8                             27
  CLUS_4                            9                              8
D31V8, multiclass
        clus
vv       DEL PEAK 23(22Q12.2) MUTATED DEL PEAK 23(22Q12.2) WILD-TYPE
  CLUS_1                           10                             17
  CLUS_2                            9                             36
  CLUS_3                            2                             10
  CLUS_4                            9                             24

Clustering(32) Variable = Del Peak 24(Xq21.31) mutation analysis
D32V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(XQ21.31) MUTATED      1    1
  DEL PEAK 24(XQ21.31) WILD-TYPE    6    8
        clus
vv       DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            1                              8
D32V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 24(XQ21.31) MUTATED"
clus
  DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE 
                             2                             14 
                    TCGA-AL-3467                     TCGA-AL-3468 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
                    TCGA-AL-3471                     TCGA-AL-3472 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
                    TCGA-AL-3473                     TCGA-B3-3925 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
                    TCGA-B3-4103                     TCGA-B3-4104 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
                    TCGA-B9-4113                     TCGA-B9-4114 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
                    TCGA-B9-4115                     TCGA-B9-4116 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
                    TCGA-B9-4117                     TCGA-B9-4617 
"DEL PEAK 24(XQ21.31) WILD-TYPE" "DEL PEAK 24(XQ21.31) WILD-TYPE" 
D32V3, multiclass
D32V4, multiclass
        clus
vv       DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            3                             50
  CLUS_3                           10                             21
D32V5, multiclass
        clus
vv       DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            9                             15
  CLUS_3                            1                             24
D32V6, multiclass
        clus
vv       DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            2                             35
  CLUS_3                            5                             16
D32V7, multiclass
        clus
vv       DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            7                             31
  CLUS_3                            4                             31
  CLUS_4                            3                             14
D32V8, multiclass
        clus
vv       DEL PEAK 24(XQ21.31) MUTATED DEL PEAK 24(XQ21.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            8                             37
  CLUS_3                            2                             10
  CLUS_4                            4                             29

Clustering(33) Variable = Del Peak 25(Xq28) mutation analysis
D33V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 25(XQ28) MUTATED      1    1
  DEL PEAK 25(XQ28) WILD-TYPE    6    8
        clus
vv       DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE
  CLUS_1                         1                           6
  CLUS_2                         1                           8
D33V2, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 25(XQ28) MUTATED"
clus
  DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE 
                          2                          14 
                 TCGA-AL-3467                  TCGA-AL-3468 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
                 TCGA-AL-3471                  TCGA-AL-3472 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
                 TCGA-AL-3473                  TCGA-B3-3925 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
                 TCGA-B3-4103                  TCGA-B3-4104 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
                 TCGA-B9-4113                  TCGA-B9-4114 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
                 TCGA-B9-4115                  TCGA-B9-4116 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
                 TCGA-B9-4117                  TCGA-B9-4617 
"DEL PEAK 25(XQ28) WILD-TYPE" "DEL PEAK 25(XQ28) WILD-TYPE" 
D33V3, multiclass
D33V4, multiclass
        clus
vv       DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         4                          49
  CLUS_3                         8                          23
D33V5, multiclass
        clus
vv       DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          17
  CLUS_3                         1                          24
D33V6, multiclass
        clus
vv       DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE
  CLUS_1                         4                          14
  CLUS_2                         3                          34
  CLUS_3                         4                          17
D33V7, multiclass
        clus
vv       DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          31
  CLUS_3                         5                          30
  CLUS_4                         1                          16
D33V8, multiclass
        clus
vv       DEL PEAK 25(XQ28) MUTATED DEL PEAK 25(XQ28) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          38
  CLUS_3                         1                          11
  CLUS_4                         5                          28
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
