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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvs_onlysig.2.4054/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/399204/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-WT/3157293/1.GDAC_mergedClustering.Finished/SKCM-WT.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-WT", "-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-WT"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=35, in cluster file=35, common to both=35
[1] 20 35
[1] "Amp Peak  1(1p12) mutation analysis"
[1] 3
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         13                          22 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         13                          22 
[1] "Amp Peak  2(1q44) mutation analysis"
[1] 3
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         20                          15 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         20                          15 
[1] "Amp Peak  3(4q12) mutation analysis"
[1] 3
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                         12                          23 
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                         12                          23 
[1] "Amp Peak  4(5p15.33) mutation analysis"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            13                             22 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            13                             22 
[1] "Amp Peak  5(5q35.3) mutation analysis"
[1] 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            8                            27 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            8                            27 
[1] "Amp Peak  6(8q11.21) mutation analysis"
[1] 3
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                            16                             19 
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                            16                             19 
[1] "Amp Peak  7(11q13.3) mutation analysis"
[1] 3
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                            10                             25 
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                            10                             25 
[1] "Amp Peak  8(11q13.3) mutation analysis"
[1] 3
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                            10                             25 
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                            10                             25 
[1] "Amp Peak  9(12q14.1) mutation analysis"
[1] 3
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            12                             23 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            12                             23 
[1] "Amp Peak 10(17q25.3) mutation analysis"
[1] 3
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                            16                             19 
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                            16                             19 
[1] "Amp Peak 11(22q13.1) mutation analysis"
[1] 3
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                            17                             18 
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                            17                             18 
[1] "Amp Peak 12(Xq28) mutation analysis"
[1] 3
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         10                          25 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         10                          25 
[1] "Del Peak 1(2q37.3) mutation analysis"
[1] 3
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                          12                           23 
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                          12                           23 
[1] "Del Peak 2(4q34.3) mutation analysis"
[1] 3
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           9                           26 
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           9                           26 
[1] "Del Peak 3(5p15.31) mutation analysis"
[1] 3
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                            8                            27 
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                            8                            27 
[1] "Del Peak 4(9p21.3) mutation analysis"
[1] 3
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                          21                           14 
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                          21                           14 
[1] "Del Peak 5(10q26.3) mutation analysis"
[1] 3
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                           18                            17 
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                           18                            17 
[1] "Del Peak 6(11q23.3) mutation analysis"
[1] 3
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                           22                            13 
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                           22                            13 
[1] "Del Peak 7(15q14) mutation analysis"
[1] 3
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                         11                          24 
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                         11                          24 
[1] "Del Peak 8(16p13.3) mutation analysis"
[1] 3
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                            9                            26 
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                            9                            26 
[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 35 columns.

Variable 1:'CN_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=2,	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 35 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=2, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=2, 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(1p12) mutation analysis
D1V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      8    5
  AMP PEAK  1(1P12) WILD-TYPE   10   12
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         8                          10
  CLUS_2                         5                          12
D1V2, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      8    5
  AMP PEAK  1(1P12) WILD-TYPE   12   10
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         8                          12
  CLUS_2                         5                          10
D1V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      4    4
  AMP PEAK  1(1P12) WILD-TYPE    7    5
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         4                           7
  CLUS_2                         4                           5
D1V4, multiclass
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         3                           4
  CLUS_2                         3                           2
  CLUS_3                         2                           6
D1V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      4    8
  AMP PEAK  1(1P12) WILD-TYPE    8   13
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         4                           8
  CLUS_2                         8                          13
D1V6, multiclass
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         2                           2
  CLUS_2                         3                           8
  CLUS_3                         7                          11
D1V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      7    5
  AMP PEAK  1(1P12) WILD-TYPE   12   10
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         7                          12
  CLUS_2                         5                          10
D1V8, multiclass
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  CLUS_1                         4                           7
  CLUS_2                         5                           6
  CLUS_3                         3                           9

Clustering(2) Variable = Amp Peak  2(1q44) mutation analysis
D2V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED     13    7
  AMP PEAK  2(1Q44) WILD-TYPE    5   10
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                        13                           5
  CLUS_2                         7                          10
D2V2, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED     13    7
  AMP PEAK  2(1Q44) WILD-TYPE    7    8
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                        13                           7
  CLUS_2                         7                           8
D2V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED      6    5
  AMP PEAK  2(1Q44) WILD-TYPE    5    4
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                         6                           5
  CLUS_2                         5                           4
D2V4, multiclass
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                         4                           3
  CLUS_2                         3                           2
  CLUS_3                         4                           4
D2V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED      5   14
  AMP PEAK  2(1Q44) WILD-TYPE    7    7
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                         5                           7
  CLUS_2                        14                           7
D2V6, multiclass
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                         4                           0
  CLUS_2                         4                           7
  CLUS_3                        11                           7
D2V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED     13    7
  AMP PEAK  2(1Q44) WILD-TYPE    6    8
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                        13                           6
  CLUS_2                         7                           8
D2V8, multiclass
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  CLUS_1                         4                           7
  CLUS_2                         9                           2
  CLUS_3                         7                           5

Clustering(3) Variable = Amp Peak  3(4q12) mutation analysis
D3V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(4Q12) MUTATED      8    4
  AMP PEAK  3(4Q12) WILD-TYPE   10   13
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         8                          10
  CLUS_2                         4                          13
D3V2, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(4Q12) MUTATED      8    4
  AMP PEAK  3(4Q12) WILD-TYPE   12   11
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         8                          12
  CLUS_2                         4                          11
D3V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(4Q12) MUTATED      6    2
  AMP PEAK  3(4Q12) WILD-TYPE    5    7
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         6                           5
  CLUS_2                         2                           7
D3V4, multiclass
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         2                           5
  CLUS_2                         4                           1
  CLUS_3                         2                           6
D3V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(4Q12) MUTATED      4    7
  AMP PEAK  3(4Q12) WILD-TYPE    8   14
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         4                           8
  CLUS_2                         7                          14
D3V6, multiclass
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         2                           2
  CLUS_2                         3                           8
  CLUS_3                         6                          12
D3V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(4Q12) MUTATED      8    4
  AMP PEAK  3(4Q12) WILD-TYPE   11   11
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         8                          11
  CLUS_2                         4                          11
D3V8, multiclass
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  CLUS_1                         2                           9
  CLUS_2                         6                           5
  CLUS_3                         4                           8

Clustering(4) Variable = Amp Peak  4(5p15.33) mutation analysis
D4V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     10    3
  AMP PEAK  4(5P15.33) WILD-TYPE    8   14
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                           10                              8
  CLUS_2                            3                             14
D4V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      9    4
  AMP PEAK  4(5P15.33) WILD-TYPE   11   11
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            9                             11
  CLUS_2                            4                             11
D4V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      5    1
  AMP PEAK  4(5P15.33) WILD-TYPE    6    8
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            5                              6
  CLUS_2                            1                              8
D4V4, multiclass
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            2                              3
  CLUS_3                            3                              5
D4V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      3   10
  AMP PEAK  4(5P15.33) WILD-TYPE    9   11
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            3                              9
  CLUS_2                           10                             11
D4V6, multiclass
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                            3                              8
  CLUS_3                            8                             10
D4V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      9    3
  AMP PEAK  4(5P15.33) WILD-TYPE   10   12
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            3                             12
D4V8, multiclass
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  CLUS_1                            1                             10
  CLUS_2                            5                              6
  CLUS_3                            6                              6

Clustering(5) Variable = Amp Peak  5(5q35.3) mutation analysis
D5V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      7    1
  AMP PEAK  5(5Q35.3) WILD-TYPE   11   16
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           7                            11
  CLUS_2                           1                            16
D5V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      7    1
  AMP PEAK  5(5Q35.3) WILD-TYPE   13   14
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           7                            13
  CLUS_2                           1                            14
D5V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      3    0
  AMP PEAK  5(5Q35.3) WILD-TYPE    8    9
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           3                             8
  CLUS_2                           0                             9
D5V4, multiclass
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           1                             4
  CLUS_3                           2                             6
D5V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      2    5
  AMP PEAK  5(5Q35.3) WILD-TYPE   10   16
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           2                            10
  CLUS_2                           5                            16
D5V6, multiclass
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           2                             9
  CLUS_3                           5                            13
D5V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      6    1
  AMP PEAK  5(5Q35.3) WILD-TYPE   13   14
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           1                            14
D5V8, multiclass
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  CLUS_1                           0                            11
  CLUS_2                           3                             8
  CLUS_3                           4                             8

Clustering(6) Variable = Amp Peak  6(8q11.21) mutation analysis
D6V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q11.21) MUTATED     10    6
  AMP PEAK  6(8Q11.21) WILD-TYPE    8   11
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                           10                              8
  CLUS_2                            6                             11
D6V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q11.21) MUTATED     11    5
  AMP PEAK  6(8Q11.21) WILD-TYPE    9   10
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                           11                              9
  CLUS_2                            5                             10
D6V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q11.21) MUTATED      6    5
  AMP PEAK  6(8Q11.21) WILD-TYPE    5    4
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                            6                              5
  CLUS_2                            5                              4
D6V4, multiclass
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                            4                              3
  CLUS_2                            4                              1
  CLUS_3                            3                              5
D6V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q11.21) MUTATED      2   13
  AMP PEAK  6(8Q11.21) WILD-TYPE   10    8
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                            2                             10
  CLUS_2                           13                              8
D6V6, multiclass
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                            3                              1
  CLUS_2                            2                              9
  CLUS_3                           10                              8
D6V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q11.21) MUTATED      7    8
  AMP PEAK  6(8Q11.21) WILD-TYPE   12    7
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                            7                             12
  CLUS_2                            8                              7
D6V8, multiclass
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  CLUS_1                            5                              6
  CLUS_2                            4                              7
  CLUS_3                            6                              6

Clustering(7) Variable = Amp Peak  7(11q13.3) mutation analysis
D7V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11Q13.3) MUTATED      7    3
  AMP PEAK  7(11Q13.3) WILD-TYPE   11   14
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            3                             14
D7V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11Q13.3) MUTATED      7    3
  AMP PEAK  7(11Q13.3) WILD-TYPE   13   12
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            7                             13
  CLUS_2                            3                             12
D7V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11Q13.3) MUTATED      3    1
  AMP PEAK  7(11Q13.3) WILD-TYPE    8    8
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            3                              8
  CLUS_2                            1                              8
D7V4, multiclass
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            1                              4
  CLUS_3                            2                              6
D7V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11Q13.3) MUTATED      2    7
  AMP PEAK  7(11Q13.3) WILD-TYPE   10   14
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            2                             10
  CLUS_2                            7                             14
D7V6, multiclass
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                            2                              9
  CLUS_3                            5                             13
D7V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11Q13.3) MUTATED      6    3
  AMP PEAK  7(11Q13.3) WILD-TYPE   13   12
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            3                             12
D7V8, multiclass
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  CLUS_1                            1                             10
  CLUS_2                            2                              9
  CLUS_3                            6                              6

Clustering(8) Variable = Amp Peak  8(11q13.3) mutation analysis
D8V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11Q13.3) MUTATED      7    3
  AMP PEAK  8(11Q13.3) WILD-TYPE   11   14
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            7                             11
  CLUS_2                            3                             14
D8V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11Q13.3) MUTATED      7    3
  AMP PEAK  8(11Q13.3) WILD-TYPE   13   12
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            7                             13
  CLUS_2                            3                             12
D8V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11Q13.3) MUTATED      3    1
  AMP PEAK  8(11Q13.3) WILD-TYPE    8    8
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            3                              8
  CLUS_2                            1                              8
D8V4, multiclass
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            1                              4
  CLUS_3                            2                              6
D8V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11Q13.3) MUTATED      2    7
  AMP PEAK  8(11Q13.3) WILD-TYPE   10   14
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            2                             10
  CLUS_2                            7                             14
D8V6, multiclass
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                            2                              9
  CLUS_3                            5                             13
D8V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11Q13.3) MUTATED      6    3
  AMP PEAK  8(11Q13.3) WILD-TYPE   13   12
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            6                             13
  CLUS_2                            3                             12
D8V8, multiclass
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  CLUS_1                            1                             10
  CLUS_2                            2                              9
  CLUS_3                            6                              6

Clustering(9) Variable = Amp Peak  9(12q14.1) mutation analysis
D9V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      8    4
  AMP PEAK  9(12Q14.1) WILD-TYPE   10   13
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            8                             10
  CLUS_2                            4                             13
D9V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      8    4
  AMP PEAK  9(12Q14.1) WILD-TYPE   12   11
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            8                             12
  CLUS_2                            4                             11
D9V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      5    1
  AMP PEAK  9(12Q14.1) WILD-TYPE    6    8
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            5                              6
  CLUS_2                            1                              8
D9V4, multiclass
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            2                              3
  CLUS_3                            3                              5
D9V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      2    9
  AMP PEAK  9(12Q14.1) WILD-TYPE   10   12
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            2                             10
  CLUS_2                            9                             12
D9V6, multiclass
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                            2                              9
  CLUS_3                            7                             11
D9V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      8    4
  AMP PEAK  9(12Q14.1) WILD-TYPE   11   11
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            8                             11
  CLUS_2                            4                             11
D9V8, multiclass
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  CLUS_1                            2                              9
  CLUS_2                            5                              6
  CLUS_3                            5                              7

Clustering(10) Variable = Amp Peak 10(17q25.3) mutation analysis
D10V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17Q25.3) MUTATED     10    6
  AMP PEAK 10(17Q25.3) WILD-TYPE    8   11
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                           10                              8
  CLUS_2                            6                             11
D10V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17Q25.3) MUTATED     10    6
  AMP PEAK 10(17Q25.3) WILD-TYPE   10    9
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                           10                             10
  CLUS_2                            6                              9
D10V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17Q25.3) MUTATED      4    3
  AMP PEAK 10(17Q25.3) WILD-TYPE    7    6
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                            4                              7
  CLUS_2                            3                              6
D10V4, multiclass
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                            3                              4
  CLUS_2                            2                              3
  CLUS_3                            2                              6
D10V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17Q25.3) MUTATED      6    9
  AMP PEAK 10(17Q25.3) WILD-TYPE    6   12
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                            6                              6
  CLUS_2                            9                             12
D10V6, multiclass
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                            3                              1
  CLUS_2                            5                              6
  CLUS_3                            7                             11
D10V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17Q25.3) MUTATED      9    6
  AMP PEAK 10(17Q25.3) WILD-TYPE   10    9
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            6                              9
D10V8, multiclass
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  CLUS_1                            3                              8
  CLUS_2                            4                              7
  CLUS_3                            8                              4

Clustering(11) Variable = Amp Peak 11(22q13.1) mutation analysis
D11V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(22Q13.1) MUTATED     11    6
  AMP PEAK 11(22Q13.1) WILD-TYPE    7   11
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                           11                              7
  CLUS_2                            6                             11
D11V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(22Q13.1) MUTATED     12    5
  AMP PEAK 11(22Q13.1) WILD-TYPE    8   10
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                           12                              8
  CLUS_2                            5                             10
D11V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(22Q13.1) MUTATED      6    5
  AMP PEAK 11(22Q13.1) WILD-TYPE    5    4
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                            6                              5
  CLUS_2                            5                              4
D11V4, multiclass
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                            4                              3
  CLUS_2                            4                              1
  CLUS_3                            3                              5
D11V5, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(22Q13.1) MUTATED      4   12
  AMP PEAK 11(22Q13.1) WILD-TYPE    8    9
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                            4                              8
  CLUS_2                           12                              9
D11V6, multiclass
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                            4                              0
  CLUS_2                            3                              8
  CLUS_3                            9                              9
D11V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(22Q13.1) MUTATED      9    7
  AMP PEAK 11(22Q13.1) WILD-TYPE   10    8
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                            9                             10
  CLUS_2                            7                              8
D11V8, multiclass
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  CLUS_1                            4                              7
  CLUS_2                            4                              7
  CLUS_3                            8                              4

Clustering(12) Variable = Amp Peak 12(Xq28) mutation analysis
D12V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     10    0
  AMP PEAK 12(XQ28) WILD-TYPE    8   17
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                        10                           8
  CLUS_2                         0                          17
D12V2, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     10    0
  AMP PEAK 12(XQ28) WILD-TYPE   10   15
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                        10                          10
  CLUS_2                         0                          15
D12V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED      5    0
  AMP PEAK 12(XQ28) WILD-TYPE    6    9
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                         5                           6
  CLUS_2                         0                           9
D12V4, multiclass
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                         0                           7
  CLUS_2                         3                           2
  CLUS_3                         2                           6
D12V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED      1    8
  AMP PEAK 12(XQ28) WILD-TYPE   11   13
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                         1                          11
  CLUS_2                         8                          13
D12V6, multiclass
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                         1                           3
  CLUS_2                         1                          10
  CLUS_3                         7                          11
D12V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED      7    3
  AMP PEAK 12(XQ28) WILD-TYPE   12   12
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                         7                          12
  CLUS_2                         3                          12
D12V8, multiclass
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  CLUS_1                         0                          11
  CLUS_2                         4                           7
  CLUS_3                         6                           6

Clustering(13) Variable = Del Peak 1(2q37.3) mutation analysis
D13V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 1(2Q37.3) MUTATED      9    3
  DEL PEAK 1(2Q37.3) WILD-TYPE    9   14
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          9                            9
  CLUS_2                          3                           14
D13V2, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 1(2Q37.3) MUTATED      9    3
  DEL PEAK 1(2Q37.3) WILD-TYPE   11   12
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          9                           11
  CLUS_2                          3                           12
D13V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 1(2Q37.3) MUTATED      6    1
  DEL PEAK 1(2Q37.3) WILD-TYPE    5    8
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          6                            5
  CLUS_2                          1                            8
D13V4, multiclass
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          1                            6
  CLUS_2                          3                            2
  CLUS_3                          3                            5
D13V5, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 1(2Q37.3) MUTATED      2    9
  DEL PEAK 1(2Q37.3) WILD-TYPE   10   12
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          2                           10
  CLUS_2                          9                           12
D13V6, multiclass
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          2                            2
  CLUS_2                          2                            9
  CLUS_3                          7                           11
D13V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 1(2Q37.3) MUTATED      8    3
  DEL PEAK 1(2Q37.3) WILD-TYPE   11   12
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          8                           11
  CLUS_2                          3                           12
D13V8, multiclass
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  CLUS_1                          1                           10
  CLUS_2                          7                            4
  CLUS_3                          3                            9

Clustering(14) Variable = Del Peak 2(4q34.3) mutation analysis
D14V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 2(4Q34.3) MUTATED      5    4
  DEL PEAK 2(4Q34.3) WILD-TYPE   13   13
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          5                           13
  CLUS_2                          4                           13
D14V2, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 2(4Q34.3) MUTATED      6    3
  DEL PEAK 2(4Q34.3) WILD-TYPE   14   12
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          6                           14
  CLUS_2                          3                           12
D14V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 2(4Q34.3) MUTATED      4    2
  DEL PEAK 2(4Q34.3) WILD-TYPE    7    7
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          4                            7
  CLUS_2                          2                            7
D14V4, multiclass
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          2                            5
  CLUS_2                          1                            4
  CLUS_3                          3                            5
D14V5, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 2(4Q34.3) MUTATED      3    5
  DEL PEAK 2(4Q34.3) WILD-TYPE    9   16
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          3                            9
  CLUS_2                          5                           16
D14V6, multiclass
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          1                            3
  CLUS_2                          2                            9
  CLUS_3                          5                           13
D14V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 2(4Q34.3) MUTATED      5    4
  DEL PEAK 2(4Q34.3) WILD-TYPE   14   11
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          5                           14
  CLUS_2                          4                           11
D14V8, multiclass
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  CLUS_1                          1                           10
  CLUS_2                          6                            5
  CLUS_3                          2                           10

Clustering(15) Variable = Del Peak 3(5p15.31) mutation analysis
D15V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 3(5P15.31) MUTATED      5    3
  DEL PEAK 3(5P15.31) WILD-TYPE   13   14
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           5                            13
  CLUS_2                           3                            14
D15V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 3(5P15.31) MUTATED      4    4
  DEL PEAK 3(5P15.31) WILD-TYPE   16   11
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           4                            16
  CLUS_2                           4                            11
D15V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 3(5P15.31) MUTATED      2    1
  DEL PEAK 3(5P15.31) WILD-TYPE    9    8
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           2                             9
  CLUS_2                           1                             8
D15V4, multiclass
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           2                             3
  CLUS_3                           0                             8
D15V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 3(5P15.31) MUTATED      5    3
  DEL PEAK 3(5P15.31) WILD-TYPE    7   18
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           5                             7
  CLUS_2                           3                            18
D15V6, multiclass
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           2                             2
  CLUS_2                           4                             7
  CLUS_3                           2                            16
D15V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 3(5P15.31) MUTATED      7    1
  DEL PEAK 3(5P15.31) WILD-TYPE   12   14
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           7                            12
  CLUS_2                           1                            14
D15V8, multiclass
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  CLUS_1                           0                            11
  CLUS_2                           3                             8
  CLUS_3                           5                             7

Clustering(16) Variable = Del Peak 4(9p21.3) mutation analysis
D16V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 4(9P21.3) MUTATED     12    9
  DEL PEAK 4(9P21.3) WILD-TYPE    6    8
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                         12                            6
  CLUS_2                          9                            8
D16V2, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 4(9P21.3) MUTATED     13    8
  DEL PEAK 4(9P21.3) WILD-TYPE    7    7
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                         13                            7
  CLUS_2                          8                            7
D16V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 4(9P21.3) MUTATED      8    5
  DEL PEAK 4(9P21.3) WILD-TYPE    3    4
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                          8                            3
  CLUS_2                          5                            4
D16V4, multiclass
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                          4                            3
  CLUS_2                          4                            1
  CLUS_3                          5                            3
D16V5, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 4(9P21.3) MUTATED      6   15
  DEL PEAK 4(9P21.3) WILD-TYPE    6    6
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                          6                            6
  CLUS_2                         15                            6
D16V6, multiclass
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                          4                            0
  CLUS_2                          5                            6
  CLUS_3                         12                            6
D16V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 4(9P21.3) MUTATED     14    6
  DEL PEAK 4(9P21.3) WILD-TYPE    5    9
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                         14                            5
  CLUS_2                          6                            9
D16V8, multiclass
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  CLUS_1                          4                            7
  CLUS_2                          9                            2
  CLUS_3                          7                            5

Clustering(17) Variable = Del Peak 5(10q26.3) mutation analysis
D17V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 5(10Q26.3) MUTATED     12    6
  DEL PEAK 5(10Q26.3) WILD-TYPE    6   11
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                          12                             6
  CLUS_2                           6                            11
D17V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 5(10Q26.3) MUTATED     13    5
  DEL PEAK 5(10Q26.3) WILD-TYPE    7   10
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                          13                             7
  CLUS_2                           5                            10
D17V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 5(10Q26.3) MUTATED      5    4
  DEL PEAK 5(10Q26.3) WILD-TYPE    6    5
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                           5                             6
  CLUS_2                           4                             5
D17V4, multiclass
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                           3                             4
  CLUS_2                           4                             1
  CLUS_3                           2                             6
D17V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 5(10Q26.3) MUTATED      4   13
  DEL PEAK 5(10Q26.3) WILD-TYPE    8    8
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                           4                             8
  CLUS_2                          13                             8
D17V6, multiclass
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                           3                             1
  CLUS_2                           3                             8
  CLUS_3                          11                             7
D17V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 5(10Q26.3) MUTATED     10    7
  DEL PEAK 5(10Q26.3) WILD-TYPE    9    8
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                          10                             9
  CLUS_2                           7                             8
D17V8, multiclass
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  CLUS_1                           3                             8
  CLUS_2                           8                             3
  CLUS_3                           6                             6

Clustering(18) Variable = Del Peak 6(11q23.3) mutation analysis
D18V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 6(11Q23.3) MUTATED     14    8
  DEL PEAK 6(11Q23.3) WILD-TYPE    4    9
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                          14                             4
  CLUS_2                           8                             9
D18V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 6(11Q23.3) MUTATED     15    7
  DEL PEAK 6(11Q23.3) WILD-TYPE    5    8
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                          15                             5
  CLUS_2                           7                             8
D18V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 6(11Q23.3) MUTATED      8    4
  DEL PEAK 6(11Q23.3) WILD-TYPE    3    5
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                           8                             3
  CLUS_2                           4                             5
D18V4, multiclass
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                           3                             4
  CLUS_2                           5                             0
  CLUS_3                           4                             4
D18V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 6(11Q23.3) MUTATED      5   16
  DEL PEAK 6(11Q23.3) WILD-TYPE    7    5
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                           5                             7
  CLUS_2                          16                             5
D18V6, multiclass
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                           4                             0
  CLUS_2                           4                             7
  CLUS_3                          13                             5
D18V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 6(11Q23.3) MUTATED     14    7
  DEL PEAK 6(11Q23.3) WILD-TYPE    5    8
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                          14                             5
  CLUS_2                           7                             8
D18V8, multiclass
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  CLUS_1                           3                             8
  CLUS_2                           9                             2
  CLUS_3                           9                             3

Clustering(19) Variable = Del Peak 7(15q14) mutation analysis
D19V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 7(15Q14) MUTATED      9    2
  DEL PEAK 7(15Q14) WILD-TYPE    9   15
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         9                           9
  CLUS_2                         2                          15
D19V2, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 7(15Q14) MUTATED      9    2
  DEL PEAK 7(15Q14) WILD-TYPE   11   13
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         9                          11
  CLUS_2                         2                          13
D19V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 7(15Q14) MUTATED      6    1
  DEL PEAK 7(15Q14) WILD-TYPE    5    8
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         6                           5
  CLUS_2                         1                           8
D19V4, multiclass
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         1                           6
  CLUS_2                         2                           3
  CLUS_3                         4                           4
D19V5, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 7(15Q14) MUTATED      1    9
  DEL PEAK 7(15Q14) WILD-TYPE   11   12
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         1                          11
  CLUS_2                         9                          12
D19V6, multiclass
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         1                           3
  CLUS_2                         1                          10
  CLUS_3                         8                          10
D19V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 7(15Q14) MUTATED      7    4
  DEL PEAK 7(15Q14) WILD-TYPE   12   11
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         7                          12
  CLUS_2                         4                          11
D19V8, multiclass
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  CLUS_1                         1                          10
  CLUS_2                         6                           5
  CLUS_3                         4                           8

Clustering(20) Variable = Del Peak 8(16p13.3) mutation analysis
D20V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 8(16P13.3) MUTATED      6    3
  DEL PEAK 8(16P13.3) WILD-TYPE   12   14
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           6                            12
  CLUS_2                           3                            14
D20V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 8(16P13.3) MUTATED      5    4
  DEL PEAK 8(16P13.3) WILD-TYPE   15   11
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           5                            15
  CLUS_2                           4                            11
D20V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 8(16P13.3) MUTATED      3    0
  DEL PEAK 8(16P13.3) WILD-TYPE    8    9
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           3                             8
  CLUS_2                           0                             9
D20V4, multiclass
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           2                             3
  CLUS_3                           1                             7
D20V5, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 8(16P13.3) MUTATED      3    6
  DEL PEAK 8(16P13.3) WILD-TYPE    9   15
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           3                             9
  CLUS_2                           6                            15
D20V6, multiclass
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           3                             8
  CLUS_3                           5                            13
D20V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 8(16P13.3) MUTATED      6    2
  DEL PEAK 8(16P13.3) WILD-TYPE   13   13
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           6                            13
  CLUS_2                           2                            13
D20V8, multiclass
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  CLUS_1                           1                            10
  CLUS_2                           3                             8
  CLUS_3                           4                             8
                     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")
