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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/399186/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-All_Primary/3157297/1.GDAC_mergedClustering.Finished/SKCM-All_Primary.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-All_Primary", "-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=SKCM-All_Primary"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=58, in cluster file=46, common to both=46
[1] 20 46
[1] "Amp Peak 1(5p15.33) mutation analysis"
[1] 3
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                           13                            33 
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                           13                            33 
[1] "Amp Peak 2(8q24.3) mutation analysis"
[1] 3
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                          23                           23 
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                          23                           23 
[1] "Amp Peak 3(11q14.1) mutation analysis"
[1] 3
  AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE 
                            7                            39 
  AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE 
                            7                            39 
[1] "Amp Peak 4(13q31.3) mutation analysis"
[1] 3
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                           14                            32 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                           14                            32 
[1] "Del Peak  1(1p22.1) mutation analysis"
[1] 3
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                           10                            36 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                           10                            36 
[1] "Del Peak  2(1q41) mutation analysis"
[1] 3
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          6                          40 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          6                          40 
[1] "Del Peak  3(4q34.3) mutation analysis"
[1] 3
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                           13                            33 
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                           13                            33 
[1] "Del Peak  4(5q31.3) mutation analysis"
[1] 3
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                           15                            31 
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                           15                            31 
[1] "Del Peak  5(6q14.1) mutation analysis"
[1] 3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                           22                            24 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                           22                            24 
[1] "Del Peak  6(6q27) mutation analysis"
[1] 3
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                         22                          24 
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                         22                          24 
[1] "Del Peak  7(6q27) mutation analysis"
[1] 3
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                         22                          24 
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                         22                          24 
[1] "Del Peak  8(9p24.2) mutation analysis"
[1] 3
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                           32                            14 
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                           32                            14 
[1] "Del Peak  9(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                           35                            11 
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                           35                            11 
[1] "Del Peak 10(10p15.3) mutation analysis"
[1] 3
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                            29                             17 
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                            29                             17 
[1] "Del Peak 11(10q23.31) mutation analysis"
[1] 3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                             29                              17 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                             29                              17 
[1] "Del Peak 12(11q24.3) mutation analysis"
[1] 3
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                            22                             24 
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                            22                             24 
[1] "Del Peak 13(12q24.32) mutation analysis"
[1] 3
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                             11                              35 
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                             11                              35 
[1] "Del Peak 14(15q15.1) mutation analysis"
[1] 3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                            11                             35 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                            11                             35 
[1] "Del Peak 15(16q23.3) mutation analysis"
[1] 3
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                            17                             29 
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                            17                             29 
[1] "Del Peak 16(22q12.1) mutation analysis"
[1] 3
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                            10                             36 
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                            10                             36 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 46 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 46 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(5p15.33) mutation analysis
D1V1, multiclass
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           5                             8
  CLUS_3                           4                            15
D1V2, multiclass
D1V3, multiclass
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           1                             4
  CLUS_3                           2                             5
D1V4, multiclass
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           2                             5
  CLUS_2                           1                             4
  CLUS_3                           3                             6
D1V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(5P15.33) MUTATED      7    6
  AMP PEAK 1(5P15.33) WILD-TYPE   20   10
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           7                            20
  CLUS_2                           6                            10
D1V6, multiclass
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           2                             1
  CLUS_3                           7                            19
D1V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(5P15.33) MUTATED      7    6
  AMP PEAK 1(5P15.33) WILD-TYPE   14   18
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           7                            14
  CLUS_2                           6                            18
D1V8, multiclass
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                           2                             7
  CLUS_3                           7                            11

Clustering(2) Variable = Amp Peak 2(8q24.3) mutation analysis
D2V1, multiclass
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                          4                           10
  CLUS_2                         13                            0
  CLUS_3                          6                           13
D2V2, multiclass
D2V3, multiclass
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                          5                            4
  CLUS_2                          1                            4
  CLUS_3                          4                            3
D2V4, multiclass
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                          4                            3
  CLUS_2                          1                            4
  CLUS_3                          5                            4
D2V5, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(8Q24.3) MUTATED     12    9
  AMP PEAK 2(8Q24.3) WILD-TYPE   15    7
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                         12                           15
  CLUS_2                          9                            7
D2V6, multiclass
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                          7                            7
  CLUS_2                          2                            1
  CLUS_3                         12                           14
D2V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(8Q24.3) MUTATED     13   10
  AMP PEAK 2(8Q24.3) WILD-TYPE    8   14
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                         13                            8
  CLUS_2                         10                           14
D2V8, multiclass
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  CLUS_1                         11                            7
  CLUS_2                          4                            5
  CLUS_3                          8                           10

Clustering(3) Variable = Amp Peak 3(11q14.1) mutation analysis
D3V1, multiclass
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           2                            12
  CLUS_2                           4                             9
  CLUS_3                           1                            18
D3V2, multiclass
D3V3, multiclass
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           2                             7
  CLUS_2                           0                             5
  CLUS_3                           1                             6
D3V4, multiclass
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           0                             5
  CLUS_3                           2                             7
D3V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11Q14.1) MUTATED      6    1
  AMP PEAK 3(11Q14.1) WILD-TYPE   21   15
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           6                            21
  CLUS_2                           1                            15
D3V6, multiclass
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           0                            14
  CLUS_2                           1                             2
  CLUS_3                           6                            20
D3V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11Q14.1) MUTATED      4    3
  AMP PEAK 3(11Q14.1) WILD-TYPE   17   21
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           4                            17
  CLUS_2                           3                            21
D3V8, multiclass
        clus
vv       AMP PEAK 3(11Q14.1) MUTATED AMP PEAK 3(11Q14.1) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                           2                             7
  CLUS_3                           1                            17

Clustering(4) Variable = Amp Peak 4(13q31.3) mutation analysis
D4V1, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           8                             6
  CLUS_2                           3                            10
  CLUS_3                           3                            16
D4V2, multiclass
D4V3, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           1                             4
  CLUS_3                           3                             4
D4V4, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           3                             4
  CLUS_2                           1                             4
  CLUS_3                           3                             6
D4V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(13Q31.3) MUTATED      8    5
  AMP PEAK 4(13Q31.3) WILD-TYPE   19   11
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           8                            19
  CLUS_2                           5                            11
D4V6, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           1                             2
  CLUS_3                           8                            18
D4V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(13Q31.3) MUTATED      8    5
  AMP PEAK 4(13Q31.3) WILD-TYPE   13   19
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           8                            13
  CLUS_2                           5                            19
D4V8, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           2                            16
  CLUS_2                           2                             7
  CLUS_3                           9                             9

Clustering(5) Variable = Del Peak  1(1p22.1) mutation analysis
D5V1, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           5                             9
  CLUS_2                           3                            10
  CLUS_3                           2                            17
D5V2, multiclass
D5V3, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           4                             5
  CLUS_2                           0                             5
  CLUS_3                           1                             6
D5V4, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           0                             5
  CLUS_3                           4                             5
D5V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      7    3
  DEL PEAK  1(1P22.1) WILD-TYPE   20   13
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           7                            20
  CLUS_2                           3                            13
D5V6, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           2                            12
  CLUS_2                           1                             2
  CLUS_3                           7                            19
D5V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      7    3
  DEL PEAK  1(1P22.1) WILD-TYPE   14   21
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           7                            14
  CLUS_2                           3                            21
D5V8, multiclass
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           1                             8
  CLUS_3                           4                            14

Clustering(6) Variable = Del Peak  2(1q41) mutation analysis
D6V1, multiclass
        clus
vv       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  CLUS_1                         2                          12
  CLUS_2                         2                          11
  CLUS_3                         2                          17
D6V2, multiclass
D6V3, multiclass
[1] "Remove cluster labels:"    "DEL PEAK  2(1Q41) MUTATED"
clus
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          1                          20 
                 TCGA-BF-A1PU                  TCGA-BF-A1PX 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-BF-A1PZ                  TCGA-EB-A1NK 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A24C                  TCGA-EB-A24D 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A299                  TCGA-ER-A194 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-ER-A196                  TCGA-ER-A19K 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-ER-A19T                  TCGA-ER-A2NB 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-ER-A2NF                  TCGA-FS-A1ZN 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GF-A2C7                  TCGA-GN-A263 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26C 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-HR-A2OG                  TCGA-HR-A2OH 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
D6V4, multiclass
[1] "Remove cluster labels:"    "DEL PEAK  2(1Q41) MUTATED"
clus
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          1                          20 
                 TCGA-BF-A1PU                  TCGA-BF-A1PX 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-BF-A1PZ                  TCGA-EB-A1NK 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A24C                  TCGA-EB-A24D 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A299                  TCGA-ER-A194 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-ER-A196                  TCGA-ER-A19K 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-ER-A19T                  TCGA-ER-A2NB 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-ER-A2NF                  TCGA-FS-A1ZN 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GF-A2C7                  TCGA-GN-A263 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26C 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-HR-A2OG                  TCGA-HR-A2OH 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
D6V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED      5    0
  DEL PEAK  2(1Q41) WILD-TYPE   22   16
        clus
vv       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  CLUS_1                         5                          22
  CLUS_2                         0                          16
D6V6, multiclass
        clus
vv       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  CLUS_1                         0                          14
  CLUS_2                         0                           3
  CLUS_3                         5                          21
D6V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED      4    2
  DEL PEAK  2(1Q41) WILD-TYPE   17   22
        clus
vv       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  CLUS_1                         4                          17
  CLUS_2                         2                          22
D6V8, multiclass
        clus
vv       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  CLUS_1                         1                          17
  CLUS_2                         1                           8
  CLUS_3                         4                          14

Clustering(7) Variable = Del Peak  3(4q34.3) mutation analysis
D7V1, multiclass
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                           6                             8
  CLUS_2                           1                            12
  CLUS_3                           6                            13
D7V2, multiclass
D7V3, multiclass
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                           4                             5
  CLUS_2                           0                             5
  CLUS_3                           1                             6
D7V4, multiclass
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           0                             5
  CLUS_3                           4                             5
D7V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(4Q34.3) MUTATED     10    3
  DEL PEAK  3(4Q34.3) WILD-TYPE   17   13
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                          10                            17
  CLUS_2                           3                            13
D7V6, multiclass
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                           3                            11
  CLUS_2                           1                             2
  CLUS_3                           9                            17
D7V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(4Q34.3) MUTATED      8    5
  DEL PEAK  3(4Q34.3) WILD-TYPE   13   19
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                           8                            13
  CLUS_2                           5                            19
D7V8, multiclass
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  CLUS_1                           6                            12
  CLUS_2                           2                             7
  CLUS_3                           5                            13

Clustering(8) Variable = Del Peak  4(5q31.3) mutation analysis
D8V1, multiclass
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           6                             8
  CLUS_2                           4                             9
  CLUS_3                           5                            14
D8V2, multiclass
D8V3, multiclass
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           3                             6
  CLUS_2                           3                             2
  CLUS_3                           3                             4
D8V4, multiclass
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           3                             4
  CLUS_2                           3                             2
  CLUS_3                           3                             6
D8V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(5Q31.3) MUTATED      7    7
  DEL PEAK  4(5Q31.3) WILD-TYPE   20    9
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           7                            20
  CLUS_2                           7                             9
D8V6, multiclass
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           7                             7
  CLUS_2                           0                             3
  CLUS_3                           7                            19
D8V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(5Q31.3) MUTATED      5    9
  DEL PEAK  4(5Q31.3) WILD-TYPE   16   15
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           5                            16
  CLUS_2                           9                            15
D8V8, multiclass
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  CLUS_1                           7                            11
  CLUS_2                           3                             6
  CLUS_3                           4                            14

Clustering(9) Variable = Del Peak  5(6q14.1) mutation analysis
D9V1, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                          10                             3
  CLUS_3                           8                            11
D9V2, multiclass
D9V3, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           4                             5
  CLUS_2                           2                             3
  CLUS_3                           3                             4
D9V4, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           3                             4
  CLUS_2                           2                             3
  CLUS_3                           4                             5
D9V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED     14    6
  DEL PEAK  5(6Q14.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                          14                            13
  CLUS_2                           6                            10
D9V6, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           3                             0
  CLUS_3                          13                            13
D9V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED     11   11
  DEL PEAK  5(6Q14.1) WILD-TYPE   10   13
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                          11                            10
  CLUS_2                          11                            13
D9V8, multiclass
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  CLUS_1                           8                            10
  CLUS_2                           5                             4
  CLUS_3                           9                             9

Clustering(10) Variable = Del Peak  6(6q27) mutation analysis
D10V1, multiclass
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                         3                          11
  CLUS_2                        11                           2
  CLUS_3                         8                          11
D10V2, multiclass
D10V3, multiclass
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                         3                           6
  CLUS_2                         1                           4
  CLUS_3                         3                           4
D10V4, multiclass
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                         3                           4
  CLUS_2                         1                           4
  CLUS_3                         3                           6
D10V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(6Q27) MUTATED     13    7
  DEL PEAK  6(6Q27) WILD-TYPE   14    9
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                        13                          14
  CLUS_2                         7                           9
D10V6, multiclass
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                         5                           9
  CLUS_2                         2                           1
  CLUS_3                        13                          13
D10V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(6Q27) MUTATED     11   11
  DEL PEAK  6(6Q27) WILD-TYPE   10   13
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                        11                          10
  CLUS_2                        11                          13
D10V8, multiclass
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  CLUS_1                         7                          11
  CLUS_2                         4                           5
  CLUS_3                        11                           7

Clustering(11) Variable = Del Peak  7(6q27) mutation analysis
D11V1, multiclass
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                         3                          11
  CLUS_2                        11                           2
  CLUS_3                         8                          11
D11V2, multiclass
D11V3, multiclass
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                         3                           6
  CLUS_2                         1                           4
  CLUS_3                         3                           4
D11V4, multiclass
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                         3                           4
  CLUS_2                         1                           4
  CLUS_3                         3                           6
D11V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(6Q27) MUTATED     13    7
  DEL PEAK  7(6Q27) WILD-TYPE   14    9
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                        13                          14
  CLUS_2                         7                           9
D11V6, multiclass
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                         5                           9
  CLUS_2                         2                           1
  CLUS_3                        13                          13
D11V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(6Q27) MUTATED     11   11
  DEL PEAK  7(6Q27) WILD-TYPE   10   13
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                        11                          10
  CLUS_2                        11                          13
D11V8, multiclass
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  CLUS_1                         7                          11
  CLUS_2                         4                           5
  CLUS_3                        11                           7

Clustering(12) Variable = Del Peak  8(9p24.2) mutation analysis
D12V1, multiclass
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                          13                             1
  CLUS_2                          10                             3
  CLUS_3                           9                            10
D12V2, multiclass
D12V3, multiclass
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                           4                             5
  CLUS_2                           4                             1
  CLUS_3                           4                             3
D12V4, multiclass
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                           4                             3
  CLUS_2                           4                             1
  CLUS_3                           4                             5
D12V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(9P24.2) MUTATED     20   11
  DEL PEAK  8(9P24.2) WILD-TYPE    7    5
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                          20                             7
  CLUS_2                          11                             5
D12V6, multiclass
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                          10                             4
  CLUS_2                           1                             2
  CLUS_3                          20                             6
D12V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(9P24.2) MUTATED     17   15
  DEL PEAK  8(9P24.2) WILD-TYPE    4    9
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                          17                             4
  CLUS_2                          15                             9
D12V8, multiclass
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  CLUS_1                          12                             6
  CLUS_2                           5                             4
  CLUS_3                          15                             3

Clustering(13) Variable = Del Peak  9(9p21.3) mutation analysis
D13V1, multiclass
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                          14                             0
  CLUS_2                          11                             2
  CLUS_3                          10                             9
D13V2, multiclass
D13V3, multiclass
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                           7                             2
  CLUS_2                           4                             1
  CLUS_3                           3                             4
D13V4, multiclass
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                           3                             4
  CLUS_2                           4                             1
  CLUS_3                           7                             2
D13V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(9P21.3) MUTATED     22   12
  DEL PEAK  9(9P21.3) WILD-TYPE    5    4
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                          22                             5
  CLUS_2                          12                             4
D13V6, multiclass
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                          11                             3
  CLUS_2                           2                             1
  CLUS_3                          21                             5
D13V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(9P21.3) MUTATED     19   16
  DEL PEAK  9(9P21.3) WILD-TYPE    2    8
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                          19                             2
  CLUS_2                          16                             8
D13V8, multiclass
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  CLUS_1                          11                             7
  CLUS_2                           6                             3
  CLUS_3                          18                             0

Clustering(14) Variable = Del Peak 10(10p15.3) mutation analysis
D14V1, multiclass
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                           12                              2
  CLUS_2                           10                              3
  CLUS_3                            7                             12
D14V2, multiclass
D14V3, multiclass
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                            6                              3
  CLUS_2                            2                              3
  CLUS_3                            5                              2
D14V4, multiclass
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                            5                              2
  CLUS_2                            2                              3
  CLUS_3                            6                              3
D14V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(10P15.3) MUTATED     17   11
  DEL PEAK 10(10P15.3) WILD-TYPE   10    5
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                           17                             10
  CLUS_2                           11                              5
D14V6, multiclass
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                           10                              4
  CLUS_2                            1                              2
  CLUS_3                           17                              9
D14V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(10P15.3) MUTATED     16   13
  DEL PEAK 10(10P15.3) WILD-TYPE    5   11
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                           16                              5
  CLUS_2                           13                             11
D14V8, multiclass
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  CLUS_1                           11                              7
  CLUS_2                            6                              3
  CLUS_3                           12                              6

Clustering(15) Variable = Del Peak 11(10q23.31) mutation analysis
D15V1, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                            13                               1
  CLUS_2                             9                               4
  CLUS_3                             7                              12
D15V2, multiclass
D15V3, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             6                               3
  CLUS_2                             2                               3
  CLUS_3                             3                               4
D15V4, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             3                               4
  CLUS_2                             2                               3
  CLUS_3                             6                               3
D15V5, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED     16   12
  DEL PEAK 11(10Q23.31) WILD-TYPE   11    4
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                            16                              11
  CLUS_2                            12                               4
D15V6, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                            11                               3
  CLUS_2                             1                               2
  CLUS_3                            16                              10
D15V7, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED     15   14
  DEL PEAK 11(10Q23.31) WILD-TYPE    6   10
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                            15                               6
  CLUS_2                            14                              10
D15V8, multiclass
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  CLUS_1                             9                               9
  CLUS_2                             6                               3
  CLUS_3                            14                               4

Clustering(16) Variable = Del Peak 12(11q24.3) mutation analysis
D16V1, multiclass
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                            7                              7
  CLUS_2                            7                              6
  CLUS_3                            8                             11
D16V2, multiclass
D16V3, multiclass
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                            6                              3
  CLUS_2                            1                              4
  CLUS_3                            2                              5
D16V4, multiclass
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            1                              4
  CLUS_3                            6                              3
D16V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(11Q24.3) MUTATED     15    6
  DEL PEAK 12(11Q24.3) WILD-TYPE   12   10
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                           15                             12
  CLUS_2                            6                             10
D16V6, multiclass
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            3                              0
  CLUS_3                           14                             12
D16V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(11Q24.3) MUTATED     12   10
  DEL PEAK 12(11Q24.3) WILD-TYPE    9   14
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                           12                              9
  CLUS_2                           10                             14
D16V8, multiclass
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  CLUS_1                            9                              9
  CLUS_2                            5                              4
  CLUS_3                            8                             10

Clustering(17) Variable = Del Peak 13(12q24.32) mutation analysis
D17V1, multiclass
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             6                               8
  CLUS_2                             3                              10
  CLUS_3                             2                              17
D17V2, multiclass
D17V3, multiclass
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             5                               4
  CLUS_2                             0                               5
  CLUS_3                             1                               6
D17V4, multiclass
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             1                               6
  CLUS_2                             0                               5
  CLUS_3                             5                               4
D17V5, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 13(12Q24.32) MUTATED      6    5
  DEL PEAK 13(12Q24.32) WILD-TYPE   21   11
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             6                              21
  CLUS_2                             5                              11
D17V6, multiclass
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             4                              10
  CLUS_2                             1                               2
  CLUS_3                             6                              20
D17V7, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 13(12Q24.32) MUTATED      8    3
  DEL PEAK 13(12Q24.32) WILD-TYPE   13   21
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             8                              13
  CLUS_2                             3                              21
D17V8, multiclass
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  CLUS_1                             4                              14
  CLUS_2                             0                               9
  CLUS_3                             7                              11

Clustering(18) Variable = Del Peak 14(15q15.1) mutation analysis
D18V1, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            6                              7
  CLUS_3                            3                             16
D18V2, multiclass
D18V3, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            0                              5
  CLUS_3                            2                              5
D18V4, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            0                              5
  CLUS_3                            2                              7
D18V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      6    3
  DEL PEAK 14(15Q15.1) WILD-TYPE   21   13
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            6                             21
  CLUS_2                            3                             13
D18V6, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            1                              2
  CLUS_3                            6                             20
D18V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      5    6
  DEL PEAK 14(15Q15.1) WILD-TYPE   16   18
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            5                             16
  CLUS_2                            6                             18
D18V8, multiclass
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  CLUS_1                            4                             14
  CLUS_2                            4                              5
  CLUS_3                            3                             15

Clustering(19) Variable = Del Peak 15(16q23.3) mutation analysis
D19V1, multiclass
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                            3                             11
  CLUS_2                            6                              7
  CLUS_3                            8                             11
D19V2, multiclass
D19V3, multiclass
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                            2                              7
  CLUS_2                            2                              3
  CLUS_3                            4                              3
D19V4, multiclass
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                            4                              3
  CLUS_2                            2                              3
  CLUS_3                            2                              7
D19V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(16Q23.3) MUTATED     10    5
  DEL PEAK 15(16Q23.3) WILD-TYPE   17   11
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                           10                             17
  CLUS_2                            5                             11
D19V6, multiclass
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                            4                             10
  CLUS_2                            2                              1
  CLUS_3                            9                             17
D19V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(16Q23.3) MUTATED      8    8
  DEL PEAK 15(16Q23.3) WILD-TYPE   13   16
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                            8                             13
  CLUS_2                            8                             16
D19V8, multiclass
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            4                              5
  CLUS_3                            7                             11

Clustering(20) Variable = Del Peak 16(22q12.1) mutation analysis
D20V1, multiclass
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            4                              9
  CLUS_3                            4                             15
D20V2, multiclass
D20V3, multiclass
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            1                              8
  CLUS_2                            1                              4
  CLUS_3                            2                              5
D20V4, multiclass
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            1                              4
  CLUS_3                            1                              8
D20V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(22Q12.1) MUTATED      7    2
  DEL PEAK 16(22Q12.1) WILD-TYPE   20   14
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            7                             20
  CLUS_2                            2                             14
D20V6, multiclass
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            0                              3
  CLUS_3                            7                             19
D20V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(22Q12.1) MUTATED      6    4
  DEL PEAK 16(22Q12.1) WILD-TYPE   15   20
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            6                             15
  CLUS_2                            4                             20
D20V8, multiclass
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  CLUS_1                            3                             15
  CLUS_2                            1                              8
  CLUS_3                            6                             12
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"             "RPPA_CNMF" 
                     V4                      V5                      V6 
   "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
