
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/335531/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SARC-TP/2667025/1.GDAC_mergedClustering.Finished/SARC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SARC-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=SARC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=52, in cluster file=29, common to both=29
[1] 28 29
[1] "Amp Peak  1(1q24.3) mutation analysis"
[1] 3
  AMP PEAK  1(1Q24.3) MUTATED AMP PEAK  1(1Q24.3) WILD-TYPE 
                           10                            19 
  AMP PEAK  1(1Q24.3) MUTATED AMP PEAK  1(1Q24.3) WILD-TYPE 
                           10                            19 
[1] "Amp Peak  2(4p15.2) mutation analysis"
[1] 3
  AMP PEAK  2(4P15.2) MUTATED AMP PEAK  2(4P15.2) WILD-TYPE 
                            8                            21 
  AMP PEAK  2(4P15.2) MUTATED AMP PEAK  2(4P15.2) WILD-TYPE 
                            8                            21 
[1] "Amp Peak  3(5p14.2) mutation analysis"
[1] 3
  AMP PEAK  3(5P14.2) MUTATED AMP PEAK  3(5P14.2) WILD-TYPE 
                            8                            21 
  AMP PEAK  3(5P14.2) MUTATED AMP PEAK  3(5P14.2) WILD-TYPE 
                            8                            21 
[1] "Amp Peak  4(5p14.1) mutation analysis"
[1] 3
  AMP PEAK  4(5P14.1) MUTATED AMP PEAK  4(5P14.1) WILD-TYPE 
                            9                            20 
  AMP PEAK  4(5P14.1) MUTATED AMP PEAK  4(5P14.1) WILD-TYPE 
                            9                            20 
[1] "Amp Peak  5(6p21.1) mutation analysis"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                            7                            22 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                            7                            22 
[1] "Amp Peak  6(6q25.1) mutation analysis"
[1] 3
  AMP PEAK  6(6Q25.1) MUTATED AMP PEAK  6(6Q25.1) WILD-TYPE 
                            9                            20 
  AMP PEAK  6(6Q25.1) MUTATED AMP PEAK  6(6Q25.1) WILD-TYPE 
                            9                            20 
[1] "Amp Peak  7(7p15.3) mutation analysis"
[1] 3
  AMP PEAK  7(7P15.3) MUTATED AMP PEAK  7(7P15.3) WILD-TYPE 
                           10                            19 
  AMP PEAK  7(7P15.3) MUTATED AMP PEAK  7(7P15.3) WILD-TYPE 
                           10                            19 
[1] "Amp Peak  8(12p13.32) mutation analysis"
[1] 3
  AMP PEAK  8(12P13.32) MUTATED AMP PEAK  8(12P13.32) WILD-TYPE 
                              7                              22 
  AMP PEAK  8(12P13.32) MUTATED AMP PEAK  8(12P13.32) WILD-TYPE 
                              7                              22 
[1] "Amp Peak  9(12q14.1) mutation analysis"
[1] 3
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            14                             15 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            14                             15 
[1] "Amp Peak 10(17p11.2) mutation analysis"
[1] 3
  AMP PEAK 10(17P11.2) MUTATED AMP PEAK 10(17P11.2) WILD-TYPE 
                             7                             22 
  AMP PEAK 10(17P11.2) MUTATED AMP PEAK 10(17P11.2) WILD-TYPE 
                             7                             22 
[1] "Amp Peak 11(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 11(19P13.2) MUTATED AMP PEAK 11(19P13.2) WILD-TYPE 
                            12                             17 
  AMP PEAK 11(19P13.2) MUTATED AMP PEAK 11(19P13.2) WILD-TYPE 
                            12                             17 
[1] "Del Peak  1(1q44) mutation analysis"
[1] 3
  DEL PEAK  1(1Q44) MUTATED DEL PEAK  1(1Q44) WILD-TYPE 
                          8                          21 
  DEL PEAK  1(1Q44) MUTATED DEL PEAK  1(1Q44) WILD-TYPE 
                          8                          21 
[1] "Del Peak  2(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                           14                            15 
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                           14                            15 
[1] "Del Peak  3(3q25.1) mutation analysis"
[1] 3
  DEL PEAK  3(3Q25.1) MUTATED DEL PEAK  3(3Q25.1) WILD-TYPE 
                            9                            20 
  DEL PEAK  3(3Q25.1) MUTATED DEL PEAK  3(3Q25.1) WILD-TYPE 
                            9                            20 
[1] "Del Peak  4(4q35.1) mutation analysis"
[1] 3
  DEL PEAK  4(4Q35.1) MUTATED DEL PEAK  4(4Q35.1) WILD-TYPE 
                           13                            16 
  DEL PEAK  4(4Q35.1) MUTATED DEL PEAK  4(4Q35.1) WILD-TYPE 
                           13                            16 
[1] "Del Peak  5(5q23.3) mutation analysis"
[1] 3
  DEL PEAK  5(5Q23.3) MUTATED DEL PEAK  5(5Q23.3) WILD-TYPE 
                            6                            23 
  DEL PEAK  5(5Q23.3) MUTATED DEL PEAK  5(5Q23.3) WILD-TYPE 
                            6                            23 
[1] "Del Peak  6(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                            18 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                            18 
[1] "Del Peak  7(11p15.4) mutation analysis"
[1] 3
  DEL PEAK  7(11P15.4) MUTATED DEL PEAK  7(11P15.4) WILD-TYPE 
                            12                             17 
  DEL PEAK  7(11P15.4) MUTATED DEL PEAK  7(11P15.4) WILD-TYPE 
                            12                             17 
[1] "Del Peak  8(11q22.3) mutation analysis"
[1] 3
  DEL PEAK  8(11Q22.3) MUTATED DEL PEAK  8(11Q22.3) WILD-TYPE 
                            15                             14 
  DEL PEAK  8(11Q22.3) MUTATED DEL PEAK  8(11Q22.3) WILD-TYPE 
                            15                             14 
[1] "Del Peak  9(12p12.3) mutation analysis"
[1] 3
  DEL PEAK  9(12P12.3) MUTATED DEL PEAK  9(12P12.3) WILD-TYPE 
                             9                             20 
  DEL PEAK  9(12P12.3) MUTATED DEL PEAK  9(12P12.3) WILD-TYPE 
                             9                             20 
[1] "Del Peak 10(13q14.2) mutation analysis"
[1] 3
  DEL PEAK 10(13Q14.2) MUTATED DEL PEAK 10(13Q14.2) WILD-TYPE 
                            19                             10 
  DEL PEAK 10(13Q14.2) MUTATED DEL PEAK 10(13Q14.2) WILD-TYPE 
                            19                             10 
[1] "Del Peak 11(15q13.3) mutation analysis"
[1] 3
  DEL PEAK 11(15Q13.3) MUTATED DEL PEAK 11(15Q13.3) WILD-TYPE 
                            10                             19 
  DEL PEAK 11(15Q13.3) MUTATED DEL PEAK 11(15Q13.3) WILD-TYPE 
                            10                             19 
[1] "Del Peak 12(17p13.1) mutation analysis"
[1] 3
  DEL PEAK 12(17P13.1) MUTATED DEL PEAK 12(17P13.1) WILD-TYPE 
                             8                             21 
  DEL PEAK 12(17P13.1) MUTATED DEL PEAK 12(17P13.1) WILD-TYPE 
                             8                             21 
[1] "Del Peak 13(17q25.3) mutation analysis"
[1] 3
  DEL PEAK 13(17Q25.3) MUTATED DEL PEAK 13(17Q25.3) WILD-TYPE 
                             6                             23 
  DEL PEAK 13(17Q25.3) MUTATED DEL PEAK 13(17Q25.3) WILD-TYPE 
                             6                             23 
[1] "Del Peak 14(19q13.32) mutation analysis"
[1] 3
  DEL PEAK 14(19Q13.32) MUTATED DEL PEAK 14(19Q13.32) WILD-TYPE 
                             11                              18 
  DEL PEAK 14(19Q13.32) MUTATED DEL PEAK 14(19Q13.32) WILD-TYPE 
                             11                              18 
[1] "Del Peak 15(21q22.3) mutation analysis"
[1] 3
  DEL PEAK 15(21Q22.3) MUTATED DEL PEAK 15(21Q22.3) WILD-TYPE 
                            11                             18 
  DEL PEAK 15(21Q22.3) MUTATED DEL PEAK 15(21Q22.3) WILD-TYPE 
                            11                             18 
[1] "Del Peak 16(Xq21.1) mutation analysis"
[1] 3
  DEL PEAK 16(XQ21.1) MUTATED DEL PEAK 16(XQ21.1) WILD-TYPE 
                           15                            14 
  DEL PEAK 16(XQ21.1) MUTATED DEL PEAK 16(XQ21.1) WILD-TYPE 
                           15                            14 
[1] "Del Peak 17(Xq28) mutation analysis"
[1] 3
  DEL PEAK 17(XQ28) MUTATED DEL PEAK 17(XQ28) WILD-TYPE 
                         12                          17 
  DEL PEAK 17(XQ28) MUTATED DEL PEAK 17(XQ28) WILD-TYPE 
                         12                          17 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"              "METHLYATION_CNMF"     "MIRSEQ_CNMF"         
[4] "MIRSEQ_CHIERARCHICAL"

Input Data has 4 rows and 29 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"              "METHLYATION_CNMF"     "MIRSEQ_CNMF"         
[4] "MIRSEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 29 columns, 0 survival variables, and 4 non-survival variables.
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, 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(1q24.3) mutation analysis
D1V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.3) MUTATED      7    3
  AMP PEAK  1(1Q24.3) WILD-TYPE   11    8
        clus
vv       AMP PEAK  1(1Q24.3) MUTATED AMP PEAK  1(1Q24.3) WILD-TYPE
  CLUS_1                           7                            11
  CLUS_2                           3                             8
D1V2, multiclass
        clus
vv       AMP PEAK  1(1Q24.3) MUTATED AMP PEAK  1(1Q24.3) WILD-TYPE
  CLUS_1                           3                             8
  CLUS_2                           4                             6
  CLUS_3                           3                             5
D1V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.3) MUTATED      6    4
  AMP PEAK  1(1Q24.3) WILD-TYPE   10    9
        clus
vv       AMP PEAK  1(1Q24.3) MUTATED AMP PEAK  1(1Q24.3) WILD-TYPE
  CLUS_1                           6                            10
  CLUS_2                           4                             9
D1V4, multiclass
        clus
vv       AMP PEAK  1(1Q24.3) MUTATED AMP PEAK  1(1Q24.3) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           4                             8
  CLUS_3                           6                            10

Clustering(2) Variable = Amp Peak  2(4p15.2) mutation analysis
D2V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P15.2) MUTATED      5    3
  AMP PEAK  2(4P15.2) WILD-TYPE   13    8
        clus
vv       AMP PEAK  2(4P15.2) MUTATED AMP PEAK  2(4P15.2) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           3                             8
D2V2, multiclass
        clus
vv       AMP PEAK  2(4P15.2) MUTATED AMP PEAK  2(4P15.2) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           3                             7
  CLUS_3                           1                             7
D2V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P15.2) MUTATED      5    3
  AMP PEAK  2(4P15.2) WILD-TYPE   11   10
        clus
vv       AMP PEAK  2(4P15.2) MUTATED AMP PEAK  2(4P15.2) WILD-TYPE
  CLUS_1                           5                            11
  CLUS_2                           3                            10
D2V4, multiclass
        clus
vv       AMP PEAK  2(4P15.2) MUTATED AMP PEAK  2(4P15.2) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           3                             9
  CLUS_3                           5                            11

Clustering(3) Variable = Amp Peak  3(5p14.2) mutation analysis
D3V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5P14.2) MUTATED      6    2
  AMP PEAK  3(5P14.2) WILD-TYPE   12    9
        clus
vv       AMP PEAK  3(5P14.2) MUTATED AMP PEAK  3(5P14.2) WILD-TYPE
  CLUS_1                           6                            12
  CLUS_2                           2                             9
D3V2, multiclass
        clus
vv       AMP PEAK  3(5P14.2) MUTATED AMP PEAK  3(5P14.2) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           2                             8
  CLUS_3                           2                             6
D3V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5P14.2) MUTATED      5    3
  AMP PEAK  3(5P14.2) WILD-TYPE   11   10
        clus
vv       AMP PEAK  3(5P14.2) MUTATED AMP PEAK  3(5P14.2) WILD-TYPE
  CLUS_1                           5                            11
  CLUS_2                           3                            10
D3V4, multiclass
        clus
vv       AMP PEAK  3(5P14.2) MUTATED AMP PEAK  3(5P14.2) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           3                             9
  CLUS_3                           5                            11

Clustering(4) Variable = Amp Peak  4(5p14.1) mutation analysis
D4V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5P14.1) MUTATED      8    1
  AMP PEAK  4(5P14.1) WILD-TYPE   10   10
        clus
vv       AMP PEAK  4(5P14.1) MUTATED AMP PEAK  4(5P14.1) WILD-TYPE
  CLUS_1                           8                            10
  CLUS_2                           1                            10
D4V2, multiclass
        clus
vv       AMP PEAK  4(5P14.1) MUTATED AMP PEAK  4(5P14.1) WILD-TYPE
  CLUS_1                           2                             9
  CLUS_2                           5                             5
  CLUS_3                           2                             6
D4V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5P14.1) MUTATED      6    3
  AMP PEAK  4(5P14.1) WILD-TYPE   10   10
        clus
vv       AMP PEAK  4(5P14.1) MUTATED AMP PEAK  4(5P14.1) WILD-TYPE
  CLUS_1                           6                            10
  CLUS_2                           3                            10
D4V4, multiclass
        clus
vv       AMP PEAK  4(5P14.1) MUTATED AMP PEAK  4(5P14.1) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           3                             9
  CLUS_3                           6                            10

Clustering(5) Variable = Amp Peak  5(6p21.1) mutation analysis
D5V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      4    3
  AMP PEAK  5(6P21.1) WILD-TYPE   14    8
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  CLUS_1                           4                            14
  CLUS_2                           3                             8
D5V2, multiclass
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           3                             7
  CLUS_3                           0                             8
D5V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      5    2
  AMP PEAK  5(6P21.1) WILD-TYPE   11   11
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  CLUS_1                           5                            11
  CLUS_2                           2                            11
D5V4, multiclass
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           2                            10
  CLUS_3                           5                            11

Clustering(6) Variable = Amp Peak  6(6q25.1) mutation analysis
D6V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q25.1) MUTATED      3    6
  AMP PEAK  6(6Q25.1) WILD-TYPE   15    5
        clus
vv       AMP PEAK  6(6Q25.1) MUTATED AMP PEAK  6(6Q25.1) WILD-TYPE
  CLUS_1                           3                            15
  CLUS_2                           6                             5
D6V2, multiclass
        clus
vv       AMP PEAK  6(6Q25.1) MUTATED AMP PEAK  6(6Q25.1) WILD-TYPE
  CLUS_1                           7                             4
  CLUS_2                           2                             8
  CLUS_3                           0                             8
D6V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q25.1) MUTATED      7    2
  AMP PEAK  6(6Q25.1) WILD-TYPE    9   11
        clus
vv       AMP PEAK  6(6Q25.1) MUTATED AMP PEAK  6(6Q25.1) WILD-TYPE
  CLUS_1                           7                             9
  CLUS_2                           2                            11
D6V4, multiclass
        clus
vv       AMP PEAK  6(6Q25.1) MUTATED AMP PEAK  6(6Q25.1) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           2                            10
  CLUS_3                           7                             9

Clustering(7) Variable = Amp Peak  7(7p15.3) mutation analysis
D7V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P15.3) MUTATED      5    5
  AMP PEAK  7(7P15.3) WILD-TYPE   13    6
        clus
vv       AMP PEAK  7(7P15.3) MUTATED AMP PEAK  7(7P15.3) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           5                             6
D7V2, multiclass
        clus
vv       AMP PEAK  7(7P15.3) MUTATED AMP PEAK  7(7P15.3) WILD-TYPE
  CLUS_1                           5                             6
  CLUS_2                           5                             5
  CLUS_3                           0                             8
D7V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P15.3) MUTATED      8    2
  AMP PEAK  7(7P15.3) WILD-TYPE    8   11
        clus
vv       AMP PEAK  7(7P15.3) MUTATED AMP PEAK  7(7P15.3) WILD-TYPE
  CLUS_1                           8                             8
  CLUS_2                           2                            11
D7V4, multiclass
        clus
vv       AMP PEAK  7(7P15.3) MUTATED AMP PEAK  7(7P15.3) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           2                            10
  CLUS_3                           8                             8

Clustering(8) Variable = Amp Peak  8(12p13.32) mutation analysis
D8V1, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.32) MUTATED      3    4
  AMP PEAK  8(12P13.32) WILD-TYPE   15    7
        clus
vv       AMP PEAK  8(12P13.32) MUTATED AMP PEAK  8(12P13.32) WILD-TYPE
  CLUS_1                             3                              15
  CLUS_2                             4                               7
D8V2, multiclass
        clus
vv       AMP PEAK  8(12P13.32) MUTATED AMP PEAK  8(12P13.32) WILD-TYPE
  CLUS_1                             5                               6
  CLUS_2                             2                               8
  CLUS_3                             0                               8
D8V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.32) MUTATED      6    1
  AMP PEAK  8(12P13.32) WILD-TYPE   10   12
        clus
vv       AMP PEAK  8(12P13.32) MUTATED AMP PEAK  8(12P13.32) WILD-TYPE
  CLUS_1                             6                              10
  CLUS_2                             1                              12
D8V4, multiclass
        clus
vv       AMP PEAK  8(12P13.32) MUTATED AMP PEAK  8(12P13.32) WILD-TYPE
  CLUS_1                             0                               1
  CLUS_2                             1                              11
  CLUS_3                             6                              10

Clustering(9) Variable = Amp Peak  9(12q14.1) mutation analysis
D9V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      3   11
  AMP PEAK  9(12Q14.1) WILD-TYPE   15    0
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            3                             15
  CLUS_2                           11                              0
D9V2, multiclass
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            8                              3
  CLUS_2                            6                              4
  CLUS_3                            0                              8
D9V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED     13    1
  AMP PEAK  9(12Q14.1) WILD-TYPE    3   12
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                           13                              3
  CLUS_2                            1                             12
D9V4, multiclass
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            1                             11
  CLUS_3                           13                              3

Clustering(10) Variable = Amp Peak 10(17p11.2) mutation analysis
D10V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17P11.2) MUTATED      6    1
  AMP PEAK 10(17P11.2) WILD-TYPE   12   10
        clus
vv       AMP PEAK 10(17P11.2) MUTATED AMP PEAK 10(17P11.2) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                            1                             10
D10V2, multiclass
        clus
vv       AMP PEAK 10(17P11.2) MUTATED AMP PEAK 10(17P11.2) WILD-TYPE
  CLUS_1                            3                              8
  CLUS_2                            2                              8
  CLUS_3                            2                              6
D10V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17P11.2) MUTATED      2    5
  AMP PEAK 10(17P11.2) WILD-TYPE   14    8
        clus
vv       AMP PEAK 10(17P11.2) MUTATED AMP PEAK 10(17P11.2) WILD-TYPE
  CLUS_1                            2                             14
  CLUS_2                            5                              8
D10V4, multiclass
        clus
vv       AMP PEAK 10(17P11.2) MUTATED AMP PEAK 10(17P11.2) WILD-TYPE
  CLUS_1                            1                              0
  CLUS_2                            4                              8
  CLUS_3                            2                             14

Clustering(11) Variable = Amp Peak 11(19p13.2) mutation analysis
D11V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(19P13.2) MUTATED      6    6
  AMP PEAK 11(19P13.2) WILD-TYPE   12    5
        clus
vv       AMP PEAK 11(19P13.2) MUTATED AMP PEAK 11(19P13.2) WILD-TYPE
  CLUS_1                            6                             12
  CLUS_2                            6                              5
D11V2, multiclass
        clus
vv       AMP PEAK 11(19P13.2) MUTATED AMP PEAK 11(19P13.2) WILD-TYPE
  CLUS_1                            5                              6
  CLUS_2                            6                              4
  CLUS_3                            1                              7
D11V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(19P13.2) MUTATED      9    3
  AMP PEAK 11(19P13.2) WILD-TYPE    7   10
        clus
vv       AMP PEAK 11(19P13.2) MUTATED AMP PEAK 11(19P13.2) WILD-TYPE
  CLUS_1                            9                              7
  CLUS_2                            3                             10
D11V4, multiclass
        clus
vv       AMP PEAK 11(19P13.2) MUTATED AMP PEAK 11(19P13.2) WILD-TYPE
  CLUS_1                            1                              0
  CLUS_2                            2                             10
  CLUS_3                            9                              7

Clustering(12) Variable = Del Peak  1(1q44) mutation analysis
D12V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1Q44) MUTATED      4    4
  DEL PEAK  1(1Q44) WILD-TYPE   14    7
        clus
vv       DEL PEAK  1(1Q44) MUTATED DEL PEAK  1(1Q44) WILD-TYPE
  CLUS_1                         4                          14
  CLUS_2                         4                           7
D12V2, multiclass
        clus
vv       DEL PEAK  1(1Q44) MUTATED DEL PEAK  1(1Q44) WILD-TYPE
  CLUS_1                         3                           8
  CLUS_2                         5                           5
  CLUS_3                         0                           8
D12V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1Q44) MUTATED      5    3
  DEL PEAK  1(1Q44) WILD-TYPE   11   10
        clus
vv       DEL PEAK  1(1Q44) MUTATED DEL PEAK  1(1Q44) WILD-TYPE
  CLUS_1                         5                          11
  CLUS_2                         3                          10
D12V4, multiclass
        clus
vv       DEL PEAK  1(1Q44) MUTATED DEL PEAK  1(1Q44) WILD-TYPE
  CLUS_1                         0                           1
  CLUS_2                         3                           9
  CLUS_3                         5                          11

Clustering(13) Variable = Del Peak  2(2q37.3) mutation analysis
D13V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q37.3) MUTATED     10    4
  DEL PEAK  2(2Q37.3) WILD-TYPE    8    7
        clus
vv       DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  CLUS_1                          10                             8
  CLUS_2                           4                             7
D13V2, multiclass
        clus
vv       DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           6                             4
  CLUS_3                           4                             4
D13V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q37.3) MUTATED      6    8
  DEL PEAK  2(2Q37.3) WILD-TYPE   10    5
        clus
vv       DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  CLUS_1                           6                            10
  CLUS_2                           8                             5
D13V4, multiclass
        clus
vv       DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  CLUS_1                           1                             0
  CLUS_2                           7                             5
  CLUS_3                           6                            10

Clustering(14) Variable = Del Peak  3(3q25.1) mutation analysis
D14V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3Q25.1) MUTATED      5    4
  DEL PEAK  3(3Q25.1) WILD-TYPE   13    7
        clus
vv       DEL PEAK  3(3Q25.1) MUTATED DEL PEAK  3(3Q25.1) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           4                             7
D14V2, multiclass
        clus
vv       DEL PEAK  3(3Q25.1) MUTATED DEL PEAK  3(3Q25.1) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           4                             6
  CLUS_3                           1                             7
D14V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3Q25.1) MUTATED      7    2
  DEL PEAK  3(3Q25.1) WILD-TYPE    9   11
        clus
vv       DEL PEAK  3(3Q25.1) MUTATED DEL PEAK  3(3Q25.1) WILD-TYPE
  CLUS_1                           7                             9
  CLUS_2                           2                            11
D14V4, multiclass
        clus
vv       DEL PEAK  3(3Q25.1) MUTATED DEL PEAK  3(3Q25.1) WILD-TYPE
  CLUS_1                           1                             0
  CLUS_2                           1                            11
  CLUS_3                           7                             9

Clustering(15) Variable = Del Peak  4(4q35.1) mutation analysis
D15V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q35.1) MUTATED      8    5
  DEL PEAK  4(4Q35.1) WILD-TYPE   10    6
        clus
vv       DEL PEAK  4(4Q35.1) MUTATED DEL PEAK  4(4Q35.1) WILD-TYPE
  CLUS_1                           8                            10
  CLUS_2                           5                             6
D15V2, multiclass
        clus
vv       DEL PEAK  4(4Q35.1) MUTATED DEL PEAK  4(4Q35.1) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           7                             3
  CLUS_3                           2                             6
D15V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q35.1) MUTATED      9    4
  DEL PEAK  4(4Q35.1) WILD-TYPE    7    9
        clus
vv       DEL PEAK  4(4Q35.1) MUTATED DEL PEAK  4(4Q35.1) WILD-TYPE
  CLUS_1                           9                             7
  CLUS_2                           4                             9
D15V4, multiclass
        clus
vv       DEL PEAK  4(4Q35.1) MUTATED DEL PEAK  4(4Q35.1) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           4                             8
  CLUS_3                           9                             7

Clustering(16) Variable = Del Peak  5(5q23.3) mutation analysis
D16V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5Q23.3) MUTATED      2    4
  DEL PEAK  5(5Q23.3) WILD-TYPE   16    7
        clus
vv       DEL PEAK  5(5Q23.3) MUTATED DEL PEAK  5(5Q23.3) WILD-TYPE
  CLUS_1                           2                            16
  CLUS_2                           4                             7
D16V2, multiclass
        clus
vv       DEL PEAK  5(5Q23.3) MUTATED DEL PEAK  5(5Q23.3) WILD-TYPE
  CLUS_1                           2                             9
  CLUS_2                           3                             7
  CLUS_3                           1                             7
D16V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5Q23.3) MUTATED      3    3
  DEL PEAK  5(5Q23.3) WILD-TYPE   13   10
        clus
vv       DEL PEAK  5(5Q23.3) MUTATED DEL PEAK  5(5Q23.3) WILD-TYPE
  CLUS_1                           3                            13
  CLUS_2                           3                            10
D16V4, multiclass
        clus
vv       DEL PEAK  5(5Q23.3) MUTATED DEL PEAK  5(5Q23.3) WILD-TYPE
  CLUS_1                           0                             1
  CLUS_2                           3                             9
  CLUS_3                           3                            13

Clustering(17) Variable = Del Peak  6(9p21.3) mutation analysis
D17V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      6    5
  DEL PEAK  6(9P21.3) WILD-TYPE   12    6
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           6                            12
  CLUS_2                           5                             6
D17V2, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           5                             6
  CLUS_2                           5                             5
  CLUS_3                           1                             7
D17V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      7    4
  DEL PEAK  6(9P21.3) WILD-TYPE    9    9
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           7                             9
  CLUS_2                           4                             9
D17V4, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           1                             0
  CLUS_2                           3                             9
  CLUS_3                           7                             9

Clustering(18) Variable = Del Peak  7(11p15.4) mutation analysis
D18V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(11P15.4) MUTATED      7    5
  DEL PEAK  7(11P15.4) WILD-TYPE   11    6
        clus
vv       DEL PEAK  7(11P15.4) MUTATED DEL PEAK  7(11P15.4) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            5                              6
D18V2, multiclass
        clus
vv       DEL PEAK  7(11P15.4) MUTATED DEL PEAK  7(11P15.4) WILD-TYPE
  CLUS_1                            4                              7
  CLUS_2                            6                              4
  CLUS_3                            2                              6
D18V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(11P15.4) MUTATED      7    5
  DEL PEAK  7(11P15.4) WILD-TYPE    9    8
        clus
vv       DEL PEAK  7(11P15.4) MUTATED DEL PEAK  7(11P15.4) WILD-TYPE
  CLUS_1                            7                              9
  CLUS_2                            5                              8
D18V4, multiclass
        clus
vv       DEL PEAK  7(11P15.4) MUTATED DEL PEAK  7(11P15.4) WILD-TYPE
  CLUS_1                            1                              0
  CLUS_2                            4                              8
  CLUS_3                            7                              9

Clustering(19) Variable = Del Peak  8(11q22.3) mutation analysis
D19V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(11Q22.3) MUTATED      8    7
  DEL PEAK  8(11Q22.3) WILD-TYPE   10    4
        clus
vv       DEL PEAK  8(11Q22.3) MUTATED DEL PEAK  8(11Q22.3) WILD-TYPE
  CLUS_1                            8                             10
  CLUS_2                            7                              4
D19V2, multiclass
        clus
vv       DEL PEAK  8(11Q22.3) MUTATED DEL PEAK  8(11Q22.3) WILD-TYPE
  CLUS_1                            6                              5
  CLUS_2                            6                              4
  CLUS_3                            3                              5
D19V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(11Q22.3) MUTATED      9    6
  DEL PEAK  8(11Q22.3) WILD-TYPE    7    7
        clus
vv       DEL PEAK  8(11Q22.3) MUTATED DEL PEAK  8(11Q22.3) WILD-TYPE
  CLUS_1                            9                              7
  CLUS_2                            6                              7
D19V4, multiclass
        clus
vv       DEL PEAK  8(11Q22.3) MUTATED DEL PEAK  8(11Q22.3) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            6                              6
  CLUS_3                            9                              7

Clustering(20) Variable = Del Peak  9(12p12.3) mutation analysis
D20V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(12P12.3) MUTATED      4    5
  DEL PEAK  9(12P12.3) WILD-TYPE   14    6
        clus
vv       DEL PEAK  9(12P12.3) MUTATED DEL PEAK  9(12P12.3) WILD-TYPE
  CLUS_1                            4                             14
  CLUS_2                            5                              6
D20V2, multiclass
        clus
vv       DEL PEAK  9(12P12.3) MUTATED DEL PEAK  9(12P12.3) WILD-TYPE
  CLUS_1                            4                              7
  CLUS_2                            3                              7
  CLUS_3                            2                              6
D20V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(12P12.3) MUTATED      6    3
  DEL PEAK  9(12P12.3) WILD-TYPE   10   10
        clus
vv       DEL PEAK  9(12P12.3) MUTATED DEL PEAK  9(12P12.3) WILD-TYPE
  CLUS_1                            6                             10
  CLUS_2                            3                             10
D20V4, multiclass
        clus
vv       DEL PEAK  9(12P12.3) MUTATED DEL PEAK  9(12P12.3) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            3                              9
  CLUS_3                            6                             10

Clustering(21) Variable = Del Peak 10(13q14.2) mutation analysis
D21V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(13Q14.2) MUTATED     13    6
  DEL PEAK 10(13Q14.2) WILD-TYPE    5    5
        clus
vv       DEL PEAK 10(13Q14.2) MUTATED DEL PEAK 10(13Q14.2) WILD-TYPE
  CLUS_1                           13                              5
  CLUS_2                            6                              5
D21V2, multiclass
        clus
vv       DEL PEAK 10(13Q14.2) MUTATED DEL PEAK 10(13Q14.2) WILD-TYPE
  CLUS_1                            5                              6
  CLUS_2                            7                              3
  CLUS_3                            7                              1
D21V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(13Q14.2) MUTATED      9   10
  DEL PEAK 10(13Q14.2) WILD-TYPE    7    3
        clus
vv       DEL PEAK 10(13Q14.2) MUTATED DEL PEAK 10(13Q14.2) WILD-TYPE
  CLUS_1                            9                              7
  CLUS_2                           10                              3
D21V4, multiclass
        clus
vv       DEL PEAK 10(13Q14.2) MUTATED DEL PEAK 10(13Q14.2) WILD-TYPE
  CLUS_1                            1                              0
  CLUS_2                            9                              3
  CLUS_3                            9                              7

Clustering(22) Variable = Del Peak 11(15q13.3) mutation analysis
D22V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(15Q13.3) MUTATED      5    5
  DEL PEAK 11(15Q13.3) WILD-TYPE   13    6
        clus
vv       DEL PEAK 11(15Q13.3) MUTATED DEL PEAK 11(15Q13.3) WILD-TYPE
  CLUS_1                            5                             13
  CLUS_2                            5                              6
D22V2, multiclass
        clus
vv       DEL PEAK 11(15Q13.3) MUTATED DEL PEAK 11(15Q13.3) WILD-TYPE
  CLUS_1                            5                              6
  CLUS_2                            4                              6
  CLUS_3                            1                              7
D22V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(15Q13.3) MUTATED      8    2
  DEL PEAK 11(15Q13.3) WILD-TYPE    8   11
        clus
vv       DEL PEAK 11(15Q13.3) MUTATED DEL PEAK 11(15Q13.3) WILD-TYPE
  CLUS_1                            8                              8
  CLUS_2                            2                             11
D22V4, multiclass
        clus
vv       DEL PEAK 11(15Q13.3) MUTATED DEL PEAK 11(15Q13.3) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            2                             10
  CLUS_3                            8                              8

Clustering(23) Variable = Del Peak 12(17p13.1) mutation analysis
D23V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(17P13.1) MUTATED      7    1
  DEL PEAK 12(17P13.1) WILD-TYPE   11   10
        clus
vv       DEL PEAK 12(17P13.1) MUTATED DEL PEAK 12(17P13.1) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            1                             10
D23V2, multiclass
        clus
vv       DEL PEAK 12(17P13.1) MUTATED DEL PEAK 12(17P13.1) WILD-TYPE
  CLUS_1                            3                              8
  CLUS_2                            1                              9
  CLUS_3                            4                              4
D23V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(17P13.1) MUTATED      3    5
  DEL PEAK 12(17P13.1) WILD-TYPE   13    8
        clus
vv       DEL PEAK 12(17P13.1) MUTATED DEL PEAK 12(17P13.1) WILD-TYPE
  CLUS_1                            3                             13
  CLUS_2                            5                              8
D23V4, multiclass
        clus
vv       DEL PEAK 12(17P13.1) MUTATED DEL PEAK 12(17P13.1) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            5                              7
  CLUS_3                            3                             13

Clustering(24) Variable = Del Peak 13(17q25.3) mutation analysis
D24V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(17Q25.3) MUTATED      4    2
  DEL PEAK 13(17Q25.3) WILD-TYPE   14    9
        clus
vv       DEL PEAK 13(17Q25.3) MUTATED DEL PEAK 13(17Q25.3) WILD-TYPE
  CLUS_1                            4                             14
  CLUS_2                            2                              9
D24V2, multiclass
        clus
vv       DEL PEAK 13(17Q25.3) MUTATED DEL PEAK 13(17Q25.3) WILD-TYPE
  CLUS_1                            2                              9
  CLUS_2                            2                              8
  CLUS_3                            2                              6
D24V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(17Q25.3) MUTATED      3    3
  DEL PEAK 13(17Q25.3) WILD-TYPE   13   10
        clus
vv       DEL PEAK 13(17Q25.3) MUTATED DEL PEAK 13(17Q25.3) WILD-TYPE
  CLUS_1                            3                             13
  CLUS_2                            3                             10
D24V4, multiclass
        clus
vv       DEL PEAK 13(17Q25.3) MUTATED DEL PEAK 13(17Q25.3) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            3                              9
  CLUS_3                            3                             13

Clustering(25) Variable = Del Peak 14(19q13.32) mutation analysis
D25V1, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 14(19Q13.32) MUTATED      8    3
  DEL PEAK 14(19Q13.32) WILD-TYPE   10    8
        clus
vv       DEL PEAK 14(19Q13.32) MUTATED DEL PEAK 14(19Q13.32) WILD-TYPE
  CLUS_1                             8                              10
  CLUS_2                             3                               8
D25V2, multiclass
        clus
vv       DEL PEAK 14(19Q13.32) MUTATED DEL PEAK 14(19Q13.32) WILD-TYPE
  CLUS_1                             2                               9
  CLUS_2                             5                               5
  CLUS_3                             4                               4
D25V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 14(19Q13.32) MUTATED      5    6
  DEL PEAK 14(19Q13.32) WILD-TYPE   11    7
        clus
vv       DEL PEAK 14(19Q13.32) MUTATED DEL PEAK 14(19Q13.32) WILD-TYPE
  CLUS_1                             5                              11
  CLUS_2                             6                               7
D25V4, multiclass
        clus
vv       DEL PEAK 14(19Q13.32) MUTATED DEL PEAK 14(19Q13.32) WILD-TYPE
  CLUS_1                             1                               0
  CLUS_2                             5                               7
  CLUS_3                             5                              11

Clustering(26) Variable = Del Peak 15(21q22.3) mutation analysis
D26V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(21Q22.3) MUTATED      7    4
  DEL PEAK 15(21Q22.3) WILD-TYPE   11    7
        clus
vv       DEL PEAK 15(21Q22.3) MUTATED DEL PEAK 15(21Q22.3) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            4                              7
D26V2, multiclass
        clus
vv       DEL PEAK 15(21Q22.3) MUTATED DEL PEAK 15(21Q22.3) WILD-TYPE
  CLUS_1                            3                              8
  CLUS_2                            6                              4
  CLUS_3                            2                              6
D26V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(21Q22.3) MUTATED      7    4
  DEL PEAK 15(21Q22.3) WILD-TYPE    9    9
        clus
vv       DEL PEAK 15(21Q22.3) MUTATED DEL PEAK 15(21Q22.3) WILD-TYPE
  CLUS_1                            7                              9
  CLUS_2                            4                              9
D26V4, multiclass
        clus
vv       DEL PEAK 15(21Q22.3) MUTATED DEL PEAK 15(21Q22.3) WILD-TYPE
  CLUS_1                            0                              1
  CLUS_2                            4                              8
  CLUS_3                            7                              9

Clustering(27) Variable = Del Peak 16(Xq21.1) mutation analysis
D27V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(XQ21.1) MUTATED      9    6
  DEL PEAK 16(XQ21.1) WILD-TYPE    9    5
        clus
vv       DEL PEAK 16(XQ21.1) MUTATED DEL PEAK 16(XQ21.1) WILD-TYPE
  CLUS_1                           9                             9
  CLUS_2                           6                             5
D27V2, multiclass
        clus
vv       DEL PEAK 16(XQ21.1) MUTATED DEL PEAK 16(XQ21.1) WILD-TYPE
  CLUS_1                           4                             7
  CLUS_2                           6                             4
  CLUS_3                           5                             3
D27V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(XQ21.1) MUTATED      7    8
  DEL PEAK 16(XQ21.1) WILD-TYPE    9    5
        clus
vv       DEL PEAK 16(XQ21.1) MUTATED DEL PEAK 16(XQ21.1) WILD-TYPE
  CLUS_1                           7                             9
  CLUS_2                           8                             5
D27V4, multiclass
        clus
vv       DEL PEAK 16(XQ21.1) MUTATED DEL PEAK 16(XQ21.1) WILD-TYPE
  CLUS_1                           1                             0
  CLUS_2                           7                             5
  CLUS_3                           7                             9

Clustering(28) Variable = Del Peak 17(Xq28) mutation analysis
D28V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(XQ28) MUTATED      9    3
  DEL PEAK 17(XQ28) WILD-TYPE    9    8
        clus
vv       DEL PEAK 17(XQ28) MUTATED DEL PEAK 17(XQ28) WILD-TYPE
  CLUS_1                         9                           9
  CLUS_2                         3                           8
D28V2, multiclass
        clus
vv       DEL PEAK 17(XQ28) MUTATED DEL PEAK 17(XQ28) WILD-TYPE
  CLUS_1                         1                          10
  CLUS_2                         6                           4
  CLUS_3                         5                           3
D28V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(XQ28) MUTATED      5    7
  DEL PEAK 17(XQ28) WILD-TYPE   11    6
        clus
vv       DEL PEAK 17(XQ28) MUTATED DEL PEAK 17(XQ28) WILD-TYPE
  CLUS_1                         5                          11
  CLUS_2                         7                           6
D28V4, multiclass
        clus
vv       DEL PEAK 17(XQ28) MUTATED DEL PEAK 17(XQ28) WILD-TYPE
  CLUS_1                         0                           1
  CLUS_2                         7                           5
  CLUS_3                         5                          11
                    V1                     V2                     V3 
             "CN_CNMF"     "METHLYATION_CNMF"          "MIRSEQ_CNMF" 
                    V4 
"MIRSEQ_CHIERARCHICAL" 
> q(save="no")
