
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/347751/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP-TP/2709428/1.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=117, in cluster file=117, common to both=117
[1]  22 117
[1] "Amp Peak 1(2q32.1) mutation analysis"
[1] 3
  AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE 
                          20                           97 
  AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE 
                          20                           97 
[1] "Amp Peak 2(3p14.1) mutation analysis"
[1] 3
  AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE 
                          31                           86 
  AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE 
                          31                           86 
[1] "Amp Peak 3(5q35.2) mutation analysis"
[1] 3
  AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE 
                          15                          102 
  AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE 
                          15                          102 
[1] "Amp Peak 4(6p12.3) mutation analysis"
[1] 3
  AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE 
                           4                          113 
  AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE 
                           4                          113 
[1] "Amp Peak 5(7q22.1) mutation analysis"
[1] 3
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                          68                           49 
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                          68                           49 
[1] "Amp Peak 6(17q25.2) mutation analysis"
[1] 3
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                           80                            37 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                           80                            37 
[1] "Amp Peak 7(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           14                           103 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           14                           103 
[1] "Amp Peak 8(19q13.11) mutation analysis"
[1] 3
  AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE 
                             4                            113 
  AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE 
                             4                            113 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            25                             92 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            25                             92 
[1] "Del Peak  2(2p11.2) mutation analysis"
[1] 3
  DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE 
                            3                           114 
  DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE 
                            3                           114 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            5                           112 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            5                           112 
[1] "Del Peak  4(3p22.1) mutation analysis"
[1] 3
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                            8                           109 
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                            8                           109 
[1] "Del Peak  5(4q31.22) mutation analysis"
[1] 3
  DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE 
                            13                            104 
  DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE 
                            13                            104 
[1] "Del Peak  6(5q35.2) mutation analysis"
[1] 3
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                            8                           109 
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                            8                           109 
[1] "Del Peak  7(6q22.31) mutation analysis"
[1] 3
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                            13                            104 
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                            13                            104 
[1] "Del Peak  8(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                           18                            99 
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                           18                            99 
[1] "Del Peak  9(14q11.2) mutation analysis"
[1] 3
  DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE 
                            26                             91 
  DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE 
                            26                             91 
[1] "Del Peak 10(14q23.3) mutation analysis"
[1] 3
  DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE 
                            25                             92 
  DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE 
                            25                             92 
[1] "Del Peak 11(14q32.2) mutation analysis"
[1] 3
  DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE 
                            25                             92 
  DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE 
                            25                             92 
[1] "Del Peak 12(19q13.42) mutation analysis"
[1] 3
  DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE 
                             10                             107 
  DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE 
                             10                             107 
[1] "Del Peak 13(Xq21.31) mutation analysis"
[1] 3
  DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE 
                            17                            100 
  DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE 
                            17                            100 
[1] "Del Peak 14(Xq28) mutation analysis"
[1] 3
  DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE 
                         16                         101 
  DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE 
                         16                         101 
[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 117 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=4,	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 117 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=4, 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
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          6                           18
  CLUS_2                          2                           18
  CLUS_3                         10                           18
  CLUS_4                          2                           43
D1V4, multiclass
        clus
vv       AMP PEAK 1(2Q32.1) MUTATED AMP PEAK 1(2Q32.1) WILD-TYPE
  CLUS_1                          2                           19
  CLUS_2                          7                           20
  CLUS_3                          8                           31
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
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                         23                            1
  CLUS_2                          4                           16
  CLUS_3                          0                           28
  CLUS_4                          4                           41
D2V4, multiclass
        clus
vv       AMP PEAK 2(3P14.1) MUTATED AMP PEAK 2(3P14.1) WILD-TYPE
  CLUS_1                          3                           18
  CLUS_2                          4                           23
  CLUS_3                         14                           25
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(5q35.2) mutation analysis
D3V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(5Q35.2) MUTATED      3    0
  AMP PEAK 3(5Q35.2) WILD-TYPE    4    9
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          3                            4
  CLUS_2                          0                            9
D3V2, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          0                            4
  CLUS_2                          3                            4
  CLUS_3                          0                            5
D3V3, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          2                           22
  CLUS_2                          1                           19
  CLUS_3                          7                           21
  CLUS_4                          5                           40
D3V4, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          3                           18
  CLUS_2                          6                           21
  CLUS_3                          1                           38
D3V5, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          3                           24
  CLUS_2                          4                           20
  CLUS_3                          5                           20
D3V6, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          1                           17
  CLUS_2                          4                           33
  CLUS_3                          7                           14
D3V7, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          5                           22
  CLUS_2                          4                           34
  CLUS_3                          3                           32
  CLUS_4                          3                           14
D3V8, multiclass
        clus
vv       AMP PEAK 3(5Q35.2) MUTATED AMP PEAK 3(5Q35.2) WILD-TYPE
  CLUS_1                          8                           19
  CLUS_2                          3                           42
  CLUS_3                          1                           11
  CLUS_4                          3                           30

Clustering(4) Variable = Amp Peak 4(6p12.3) mutation analysis
D4V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(6P12.3) MUTATED      0    0
  AMP PEAK 4(6P12.3) WILD-TYPE    7    9
D4V2, multiclass
D4V3, multiclass
        clus
vv       AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE
  CLUS_1                          0                           24
  CLUS_2                          1                           19
  CLUS_3                          2                           26
  CLUS_4                          1                           44
D4V4, multiclass
        clus
vv       AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE
  CLUS_1                          0                           21
  CLUS_2                          3                           24
  CLUS_3                          1                           38
D4V5, multiclass
        clus
vv       AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE
  CLUS_1                          1                           26
  CLUS_2                          3                           21
  CLUS_3                          0                           25
D4V6, multiclass
        clus
vv       AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE
  CLUS_1                          2                           16
  CLUS_2                          1                           36
  CLUS_3                          1                           20
D4V7, multiclass
        clus
vv       AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE
  CLUS_1                          0                           27
  CLUS_2                          3                           35
  CLUS_3                          0                           35
  CLUS_4                          1                           16
D4V8, multiclass
        clus
vv       AMP PEAK 4(6P12.3) MUTATED AMP PEAK 4(6P12.3) WILD-TYPE
  CLUS_1                          0                           27
  CLUS_2                          3                           42
  CLUS_3                          1                           11
  CLUS_4                          0                           33

Clustering(5) Variable = Amp Peak 5(7q22.1) mutation analysis
D5V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q22.1) MUTATED      5    6
  AMP PEAK 5(7Q22.1) WILD-TYPE    2    3
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                          5                            2
  CLUS_2                          6                            3
D5V2, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                          3                            1
  CLUS_2                          4                            3
  CLUS_3                          4                            1
D5V3, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                         21                            3
  CLUS_2                         20                            0
  CLUS_3                          9                           19
  CLUS_4                         18                           27
D5V4, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                         11                           10
  CLUS_2                          9                           18
  CLUS_3                         28                           11
D5V5, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                         22                            5
  CLUS_2                          8                           16
  CLUS_3                         13                           12
D5V6, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                          8                           10
  CLUS_2                         29                            8
  CLUS_3                          6                           15
D5V7, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                         12                           15
  CLUS_2                         20                           18
  CLUS_3                         28                            7
  CLUS_4                          8                            9
D5V8, multiclass
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  CLUS_1                         11                           16
  CLUS_2                         23                           22
  CLUS_3                         10                            2
  CLUS_4                         24                            9

Clustering(6) Variable = Amp Peak 6(17q25.2) mutation analysis
D6V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED      6    6
  AMP PEAK 6(17Q25.2) WILD-TYPE    1    3
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                           6                             1
  CLUS_2                           6                             3
D6V2, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                           3                             1
  CLUS_2                           5                             2
  CLUS_3                           4                             1
D6V3, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                          22                             2
  CLUS_2                          20                             0
  CLUS_3                          14                            14
  CLUS_4                          24                            21
D6V4, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                          12                             9
  CLUS_2                          15                            12
  CLUS_3                          29                            10
D6V5, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                          20                             7
  CLUS_2                          13                            11
  CLUS_3                          14                            11
D6V6, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                          10                             8
  CLUS_2                          28                             9
  CLUS_3                           9                            12
D6V7, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                          19                             8
  CLUS_2                          26                            12
  CLUS_3                          25                            10
  CLUS_4                          10                             7
D6V8, multiclass
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  CLUS_1                          16                            11
  CLUS_2                          30                            15
  CLUS_3                          10                             2
  CLUS_4                          24                             9

Clustering(7) Variable = Amp Peak 7(19p13.2) mutation analysis
D7V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      0    4
  AMP PEAK 7(19P13.2) WILD-TYPE    7    5
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           4                             5
D7V2, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           1                             6
  CLUS_3                           1                             4
D7V3, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           0                            24
  CLUS_2                          11                             9
  CLUS_3                           3                            25
  CLUS_4                           0                            45
D7V4, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           0                            21
  CLUS_2                           3                            24
  CLUS_3                           6                            33
D7V5, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           7                            20
  CLUS_2                           3                            21
  CLUS_3                           1                            24
D7V6, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           3                            15
  CLUS_2                           6                            31
  CLUS_3                           2                            19
D7V7, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                           4                            34
  CLUS_3                           5                            30
  CLUS_4                           3                            14
D7V8, multiclass
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  CLUS_1                           3                            24
  CLUS_2                           4                            41
  CLUS_3                           1                            11
  CLUS_4                           6                            27

Clustering(8) Variable = Amp Peak 8(19q13.11) mutation analysis
D8V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 8(19Q13.11) MUTATED      0    0
  AMP PEAK 8(19Q13.11) WILD-TYPE    7    9
D8V2, multiclass
D8V3, multiclass
        clus
vv       AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE
  CLUS_1                            1                             23
  CLUS_2                            0                             20
  CLUS_3                            2                             26
  CLUS_4                            1                             44
D8V4, multiclass
        clus
vv       AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE
  CLUS_1                            0                             21
  CLUS_2                            3                             24
  CLUS_3                            1                             38
D8V5, multiclass
        clus
vv       AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE
  CLUS_1                            0                             27
  CLUS_2                            2                             22
  CLUS_3                            1                             24
D8V6, multiclass
        clus
vv       AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE
  CLUS_1                            1                             17
  CLUS_2                            0                             37
  CLUS_3                            2                             19
D8V7, multiclass
        clus
vv       AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            3                             35
  CLUS_3                            0                             35
  CLUS_4                            0                             17
D8V8, multiclass
        clus
vv       AMP PEAK 8(19Q13.11) MUTATED AMP PEAK 8(19Q13.11) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            3                             42
  CLUS_3                            0                             12
  CLUS_4                            0                             33

Clustering(9) Variable = Del Peak  1(1p36.31) mutation analysis
D9V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1    3
  DEL PEAK  1(1P36.31) WILD-TYPE    6    6
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            3                              6
D9V2, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            2                              5
  CLUS_3                            1                              4
D9V3, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            2                             22
  CLUS_2                            0                             20
  CLUS_3                           16                             12
  CLUS_4                            7                             38
D9V4, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            3                             18
  CLUS_2                            9                             18
  CLUS_3                            6                             33
D9V5, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                           10                             14
  CLUS_3                            3                             22
D9V6, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            4                             33
  CLUS_3                            6                             15
D9V7, 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                            6                             11
D9V8, 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                           10                             23

Clustering(10) Variable = Del Peak  2(2p11.2) mutation analysis
D10V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2P11.2) MUTATED      0    0
  DEL PEAK  2(2P11.2) WILD-TYPE    7    9
D10V2, multiclass
D10V3, multiclass
        clus
vv       DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE
  CLUS_1                           0                            24
  CLUS_2                           0                            20
  CLUS_3                           1                            27
  CLUS_4                           2                            43
D10V4, multiclass
        clus
vv       DEL PEAK  2(2P11.2) MUTATED DEL PEAK  2(2P11.2) WILD-TYPE
  CLUS_1                           0                            21
  CLUS_2                           1                            26
  CLUS_3                           2                            37
D10V5, 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" 
D10V6, 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" 
D10V7, 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
D10V8, 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(11) Variable = Del Peak  3(2q37.3) mutation analysis
D11V1, 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
D11V2, 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" 
D11V3, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           2                            22
  CLUS_2                           0                            20
  CLUS_3                           0                            28
  CLUS_4                           3                            42
D11V4, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           1                            20
  CLUS_2                           2                            25
  CLUS_3                           0                            39
D11V5, 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
D11V6, 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
D11V7, 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
D11V8, 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(12) Variable = Del Peak  4(3p22.1) mutation analysis
D12V1, 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
D12V2, 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" 
D12V3, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           0                            24
  CLUS_2                           0                            20
  CLUS_3                           7                            21
  CLUS_4                           1                            44
D12V4, multiclass
        clus
vv       DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE
  CLUS_1                           0                            21
  CLUS_2                           6                            21
  CLUS_3                           0                            39
D12V5, 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
D12V6, 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
D12V7, 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
D12V8, 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(13) Variable = Del Peak  5(4q31.22) mutation analysis
D13V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(4Q31.22) MUTATED      1    1
  DEL PEAK  5(4Q31.22) WILD-TYPE    6    8
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            1                              8
D13V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK  5(4Q31.22) MUTATED"
clus
  DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE 
                             2                             14 
                    TCGA-AL-3467                     TCGA-AL-3468 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
                    TCGA-AL-3471                     TCGA-AL-3472 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
                    TCGA-AL-3473                     TCGA-B3-3925 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
                    TCGA-B3-4103                     TCGA-B3-4104 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
                    TCGA-B9-4113                     TCGA-B9-4114 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
                    TCGA-B9-4115                     TCGA-B9-4116 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
                    TCGA-B9-4117                     TCGA-B9-4617 
"DEL PEAK  5(4Q31.22) WILD-TYPE" "DEL PEAK  5(4Q31.22) WILD-TYPE" 
D13V3, multiclass
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                            0                             20
  CLUS_3                            9                             19
  CLUS_4                            1                             44
D13V4, multiclass
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            0                             21
  CLUS_2                            8                             19
  CLUS_3                            1                             38
D13V5, multiclass
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            1                             26
  CLUS_2                            7                             17
  CLUS_3                            1                             24
D13V6, multiclass
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            3                             15
  CLUS_2                            1                             36
  CLUS_3                            5                             16
D13V7, multiclass
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            6                             32
  CLUS_3                            2                             33
  CLUS_4                            2                             15
D13V8, multiclass
        clus
vv       DEL PEAK  5(4Q31.22) MUTATED DEL PEAK  5(4Q31.22) WILD-TYPE
  CLUS_1                            4                             23
  CLUS_2                            5                             40
  CLUS_3                            2                             10
  CLUS_4                            2                             31

Clustering(14) Variable = Del Peak  6(5q35.2) mutation analysis
D14V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5Q35.2) MUTATED      0    1
  DEL PEAK  6(5Q35.2) WILD-TYPE    7    8
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           1                             8
D14V2, multiclass
[1] "Remove cluster labels:"      "DEL PEAK  6(5Q35.2) MUTATED"
clus
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                            1                            15 
                   TCGA-AL-3466                    TCGA-AL-3467 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-AL-3468                    TCGA-AL-3471 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-AL-3472                    TCGA-AL-3473 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-B3-3925                    TCGA-B3-3926 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-B3-4103                    TCGA-B9-4113 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-B9-4114                    TCGA-B9-4115 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-B9-4116                    TCGA-B9-4117 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-B9-4617 
"DEL PEAK  6(5Q35.2) WILD-TYPE" 
D14V3, multiclass
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           3                            21
  CLUS_2                           0                            20
  CLUS_3                           3                            25
  CLUS_4                           2                            43
D14V4, multiclass
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           1                            20
  CLUS_2                           6                            21
  CLUS_3                           0                            39
D14V5, multiclass
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           6                            18
  CLUS_3                           0                            25
D14V6, multiclass
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           0                            37
  CLUS_3                           1                            20
D14V7, multiclass
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                           5                            33
  CLUS_3                           1                            34
  CLUS_4                           1                            16
D14V8, multiclass
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  CLUS_1                           0                            27
  CLUS_2                           6                            39
  CLUS_3                           1                            11
  CLUS_4                           1                            32

Clustering(15) Variable = Del Peak  7(6q22.31) mutation analysis
D15V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(6Q22.31) MUTATED      0    1
  DEL PEAK  7(6Q22.31) WILD-TYPE    7    8
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            0                              7
  CLUS_2                            1                              8
D15V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK  7(6Q22.31) MUTATED"
clus
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                             1                             15 
                    TCGA-AL-3466                     TCGA-AL-3467 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-AL-3468                     TCGA-AL-3471 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-AL-3472                     TCGA-AL-3473 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-B3-3925                     TCGA-B3-4103 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-B3-4104                     TCGA-B9-4113 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-B9-4114                     TCGA-B9-4115 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-B9-4116                     TCGA-B9-4117 
"DEL PEAK  7(6Q22.31) WILD-TYPE" "DEL PEAK  7(6Q22.31) WILD-TYPE" 
                    TCGA-B9-4617 
"DEL PEAK  7(6Q22.31) WILD-TYPE" 
D15V3, multiclass
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            2                             22
  CLUS_2                            0                             20
  CLUS_3                            7                             21
  CLUS_4                            4                             41
D15V4, multiclass
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            3                             18
  CLUS_2                            6                             21
  CLUS_3                            2                             37
D15V5, multiclass
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            6                             18
  CLUS_3                            1                             24
D15V6, multiclass
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            3                             34
  CLUS_3                            2                             19
D15V7, multiclass
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            5                             33
  CLUS_3                            5                             30
  CLUS_4                            1                             16
D15V8, multiclass
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            8                             37
  CLUS_3                            0                             12
  CLUS_4                            3                             30

Clustering(16) Variable = Del Peak  8(9p21.3) mutation analysis
D16V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(9P21.3) MUTATED      1    2
  DEL PEAK  8(9P21.3) WILD-TYPE    6    7
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           2                             7
D16V2, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           2                             5
  CLUS_3                           1                             4
D16V3, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           3                            21
  CLUS_2                           0                            20
  CLUS_3                          10                            18
  CLUS_4                           5                            40
D16V4, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           4                            17
  CLUS_2                          10                            17
  CLUS_3                           0                            39
D16V5, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                          12                            12
  CLUS_3                           2                            23
D16V6, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           8                            10
  CLUS_2                           2                            35
  CLUS_3                           5                            16
D16V7, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           1                            26
  CLUS_2                          10                            28
  CLUS_3                           3                            32
  CLUS_4                           4                            13
D16V8, multiclass
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  CLUS_1                           2                            25
  CLUS_2                          12                            33
  CLUS_3                           1                            11
  CLUS_4                           3                            30

Clustering(17) Variable = Del Peak  9(14q11.2) mutation analysis
D17V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(14Q11.2) MUTATED      3    2
  DEL PEAK  9(14Q11.2) WILD-TYPE    4    7
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            3                              4
  CLUS_2                            2                              7
D17V2, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            4                              3
  CLUS_3                            1                              4
D17V3, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            5                             19
  CLUS_2                            0                             20
  CLUS_3                           19                              9
  CLUS_4                            2                             43
D17V4, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            7                             14
  CLUS_2                            6                             21
  CLUS_3                            6                             33
D17V5, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                           10                             14
  CLUS_3                            4                             21
D17V6, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            6                             31
  CLUS_3                            6                             15
D17V7, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             29
  CLUS_3                            7                             28
  CLUS_4                            5                             12
D17V8, multiclass
        clus
vv       DEL PEAK  9(14Q11.2) MUTATED DEL PEAK  9(14Q11.2) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                           10                             35
  CLUS_3                            2                             10
  CLUS_4                            7                             26

Clustering(18) Variable = Del Peak 10(14q23.3) mutation analysis
D18V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(14Q23.3) MUTATED      2    2
  DEL PEAK 10(14Q23.3) WILD-TYPE    5    7
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            2                              7
D18V2, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            3                              4
  CLUS_3                            1                              4
D18V3, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            4                             20
  CLUS_2                            0                             20
  CLUS_3                           20                              8
  CLUS_4                            1                             44
D18V4, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            7                             14
  CLUS_2                            7                             20
  CLUS_3                            5                             34
D18V5, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                           10                             14
  CLUS_3                            5                             20
D18V6, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            4                             33
  CLUS_3                            7                             14
D18V7, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             29
  CLUS_3                            6                             29
  CLUS_4                            5                             12
D18V8, multiclass
        clus
vv       DEL PEAK 10(14Q23.3) MUTATED DEL PEAK 10(14Q23.3) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                           10                             35
  CLUS_3                            2                             10
  CLUS_4                            6                             27

Clustering(19) Variable = Del Peak 11(14q32.2) mutation analysis
D19V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(14Q32.2) MUTATED      2    2
  DEL PEAK 11(14Q32.2) WILD-TYPE    5    7
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            2                              7
D19V2, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                            3                              4
  CLUS_3                            1                              4
D19V3, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            3                             21
  CLUS_2                            0                             20
  CLUS_3                           20                              8
  CLUS_4                            2                             43
D19V4, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            7                             14
  CLUS_2                            6                             21
  CLUS_3                            6                             33
D19V5, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            9                             15
  CLUS_3                            5                             20
D19V6, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                            4                             33
  CLUS_3                            7                             14
D19V7, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            5                             22
  CLUS_2                            9                             29
  CLUS_3                            6                             29
  CLUS_4                            5                             12
D19V8, multiclass
        clus
vv       DEL PEAK 11(14Q32.2) MUTATED DEL PEAK 11(14Q32.2) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                           10                             35
  CLUS_3                            2                             10
  CLUS_4                            6                             27

Clustering(20) Variable = Del Peak 12(19q13.42) mutation analysis
D20V1, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(19Q13.42) MUTATED      0    0
  DEL PEAK 12(19Q13.42) WILD-TYPE    7    9
D20V2, multiclass
D20V3, multiclass
        clus
vv       DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE
  CLUS_1                             3                              21
  CLUS_2                             3                              17
  CLUS_3                             3                              25
  CLUS_4                             1                              44
D20V4, multiclass
        clus
vv       DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE
  CLUS_1                             1                              20
  CLUS_2                             2                              25
  CLUS_3                             4                              35
D20V5, multiclass
        clus
vv       DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE
  CLUS_1                             1                              26
  CLUS_2                             2                              22
  CLUS_3                             2                              23
D20V6, multiclass
        clus
vv       DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE
  CLUS_1                             0                              18
  CLUS_2                             2                              35
  CLUS_3                             3                              18
D20V7, multiclass
        clus
vv       DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE
  CLUS_1                             4                              23
  CLUS_2                             2                              36
  CLUS_3                             2                              33
  CLUS_4                             2                              15
D20V8, multiclass
        clus
vv       DEL PEAK 12(19Q13.42) MUTATED DEL PEAK 12(19Q13.42) WILD-TYPE
  CLUS_1                             4                              23
  CLUS_2                             2                              43
  CLUS_3                             1                              11
  CLUS_4                             3                              30

Clustering(21) Variable = Del Peak 13(Xq21.31) mutation analysis
D21V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(XQ21.31) MUTATED      1    1
  DEL PEAK 13(XQ21.31) WILD-TYPE    6    8
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            1                              8
D21V2, multiclass
[1] "Remove cluster labels:"       "DEL PEAK 13(XQ21.31) MUTATED"
clus
  DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE 
                             2                             14 
                    TCGA-AL-3467                     TCGA-AL-3468 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
                    TCGA-AL-3471                     TCGA-AL-3472 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
                    TCGA-AL-3473                     TCGA-B3-3925 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
                    TCGA-B3-4103                     TCGA-B3-4104 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
                    TCGA-B9-4113                     TCGA-B9-4114 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
                    TCGA-B9-4115                     TCGA-B9-4116 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
                    TCGA-B9-4117                     TCGA-B9-4617 
"DEL PEAK 13(XQ21.31) WILD-TYPE" "DEL PEAK 13(XQ21.31) WILD-TYPE" 
D21V3, multiclass
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            4                             20
  CLUS_2                            0                             20
  CLUS_3                           11                             17
  CLUS_4                            2                             43
D21V4, multiclass
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            1                             20
  CLUS_2                           10                             17
  CLUS_3                            3                             36
D21V5, multiclass
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            2                             25
  CLUS_2                            9                             15
  CLUS_3                            1                             24
D21V6, multiclass
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            2                             35
  CLUS_3                            5                             16
D21V7, multiclass
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            7                             31
  CLUS_3                            4                             31
  CLUS_4                            3                             14
D21V8, multiclass
        clus
vv       DEL PEAK 13(XQ21.31) MUTATED DEL PEAK 13(XQ21.31) WILD-TYPE
  CLUS_1                            3                             24
  CLUS_2                            8                             37
  CLUS_3                            2                             10
  CLUS_4                            4                             29

Clustering(22) Variable = Del Peak 14(Xq28) mutation analysis
D22V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(XQ28) MUTATED      1    1
  DEL PEAK 14(XQ28) WILD-TYPE    6    8
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE
  CLUS_1                         1                           6
  CLUS_2                         1                           8
D22V2, multiclass
[1] "Remove cluster labels:"    "DEL PEAK 14(XQ28) MUTATED"
clus
  DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE 
                          2                          14 
                 TCGA-AL-3467                  TCGA-AL-3468 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
                 TCGA-AL-3471                  TCGA-AL-3472 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
                 TCGA-AL-3473                  TCGA-B3-3925 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
                 TCGA-B3-4103                  TCGA-B3-4104 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
                 TCGA-B9-4113                  TCGA-B9-4114 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
                 TCGA-B9-4115                  TCGA-B9-4116 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
                 TCGA-B9-4117                  TCGA-B9-4617 
"DEL PEAK 14(XQ28) WILD-TYPE" "DEL PEAK 14(XQ28) WILD-TYPE" 
D22V3, multiclass
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE
  CLUS_1                         4                          20
  CLUS_2                         0                          20
  CLUS_3                         9                          19
  CLUS_4                         3                          42
D22V4, multiclass
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE
  CLUS_1                         1                          20
  CLUS_2                         8                          19
  CLUS_3                         4                          35
D22V5, multiclass
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          17
  CLUS_3                         1                          24
D22V6, multiclass
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE
  CLUS_1                         4                          14
  CLUS_2                         3                          34
  CLUS_3                         4                          17
D22V7, multiclass
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(XQ28) WILD-TYPE
  CLUS_1                         3                          24
  CLUS_2                         7                          31
  CLUS_3                         5                          30
  CLUS_4                         1                          16
D22V8, multiclass
        clus
vv       DEL PEAK 14(XQ28) MUTATED DEL PEAK 14(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")
