
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/399177/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-NF1_Any_Mutants/3157448/1.GDAC_mergedClustering.Finished/SKCM-NF1_Any_Mutants.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-NF1_Any_Mutants", "-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-NF1_Any_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=31, in cluster file=31, common to both=31
[1] 19 31
[1] "Amp Peak 1(1p12) mutation analysis"
[1] 3
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                        10                         21 
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                        10                         21 
[1] "Amp Peak 2(1q44) mutation analysis"
[1] 3
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                        19                         12 
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                        19                         12 
[1] "Amp Peak 3(7p22.3) mutation analysis"
[1] 3
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                          16                           15 
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                          16                           15 
[1] "Amp Peak 4(7q36.1) mutation analysis"
[1] 3
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                          18                           13 
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                          18                           13 
[1] "Amp Peak 5(12p12.1) mutation analysis"
[1] 3
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            5                            26 
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            5                            26 
[1] "Amp Peak 6(15q26.2) mutation analysis"
[1] 3
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                           11                            20 
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                           11                            20 
[1] "Amp Peak 7(17q25.3) mutation analysis"
[1] 3
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                           16                            15 
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                           16                            15 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             7                             24 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             7                             24 
[1] "Del Peak  2(1p13.2) mutation analysis"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            9                            22 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            9                            22 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           10                            21 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           10                            21 
[1] "Del Peak  4(3q23) mutation analysis"
[1] 3
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          4                          27 
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          4                          27 
[1] "Del Peak  5(6q23.2) mutation analysis"
[1] 3
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                           14                            17 
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                           14                            17 
[1] "Del Peak  6(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           20                            11 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           20                            11 
[1] "Del Peak  7(10p15.1) mutation analysis"
[1] 3
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                            13                             18 
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                            13                             18 
[1] "Del Peak  8(10q24.33) mutation analysis"
[1] 3
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                             14                              17 
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                             14                              17 
[1] "Del Peak  9(11q24.3) mutation analysis"
[1] 3
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                            21                             10 
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                            21                             10 
[1] "Del Peak 10(13q34) mutation analysis"
[1] 3
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                           8                           23 
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                           8                           23 
[1] "Del Peak 11(14q23.3) mutation analysis"
[1] 3
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                             9                             22 
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                             9                             22 
[1] "Del Peak 12(16q12.1) mutation analysis"
[1] 3
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                            14                             17 
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                            14                             17 
[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 31 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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=6,	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 31 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=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=6, 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      4    6
  AMP PEAK 1(1P12) WILD-TYPE   12    9
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        4                         12
  CLUS_2                        6                          9
D1V2, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P12) MUTATED      6    4
  AMP PEAK 1(1P12) WILD-TYPE    8   13
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        6                          8
  CLUS_2                        4                         13
D1V3, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P12) MUTATED      1    6
  AMP PEAK 1(1P12) WILD-TYPE    6   10
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        1                          6
  CLUS_2                        6                         10
D1V4, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P12) MUTATED      1    6
  AMP PEAK 1(1P12) WILD-TYPE    3   13
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        1                          3
  CLUS_2                        6                         13
D1V5, multiclass
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        2                          6
  CLUS_2                        3                          8
  CLUS_3                        5                          7
D1V6, multiclass
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        3                          3
  CLUS_2                        2                          6
  CLUS_3                        2                          5
  CLUS_4                        3                          7
D1V7, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P12) MUTATED      5    5
  AMP PEAK 1(1P12) WILD-TYPE   11   10
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  CLUS_1                        5                         11
  CLUS_2                        5                         10
D1V8, multiclass

Clustering(2) Variable = Amp Peak 2(1q44) mutation analysis
D2V1, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q44) MUTATED      7   12
  AMP PEAK 2(1Q44) WILD-TYPE    9    3
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        7                          9
  CLUS_2                       12                          3
D2V2, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q44) MUTATED      7   12
  AMP PEAK 2(1Q44) WILD-TYPE    7    5
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        7                          7
  CLUS_2                       12                          5
D2V3, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q44) MUTATED      4   10
  AMP PEAK 2(1Q44) WILD-TYPE    3    6
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        4                          3
  CLUS_2                       10                          6
D2V4, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q44) MUTATED      2   12
  AMP PEAK 2(1Q44) WILD-TYPE    2    7
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        2                          2
  CLUS_2                       12                          7
D2V5, multiclass
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        5                          3
  CLUS_2                        5                          6
  CLUS_3                        9                          3
D2V6, multiclass
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        3                          3
  CLUS_2                        4                          4
  CLUS_3                        4                          3
  CLUS_4                        8                          2
D2V7, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q44) MUTATED      7   12
  AMP PEAK 2(1Q44) WILD-TYPE    9    3
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  CLUS_1                        7                          9
  CLUS_2                       12                          3
D2V8, multiclass

Clustering(3) Variable = Amp Peak 3(7p22.3) mutation analysis
D3V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(7P22.3) MUTATED      7    9
  AMP PEAK 3(7P22.3) WILD-TYPE    9    6
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          7                            9
  CLUS_2                          9                            6
D3V2, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(7P22.3) MUTATED      7    9
  AMP PEAK 3(7P22.3) WILD-TYPE    7    8
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          7                            7
  CLUS_2                          9                            8
D3V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(7P22.3) MUTATED      4    7
  AMP PEAK 3(7P22.3) WILD-TYPE    3    9
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          4                            3
  CLUS_2                          7                            9
D3V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(7P22.3) MUTATED      1   10
  AMP PEAK 3(7P22.3) WILD-TYPE    3    9
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          1                            3
  CLUS_2                         10                            9
D3V5, multiclass
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          5                            3
  CLUS_2                          5                            6
  CLUS_3                          6                            6
D3V6, multiclass
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          3                            3
  CLUS_2                          4                            4
  CLUS_3                          3                            4
  CLUS_4                          6                            4
D3V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(7P22.3) MUTATED      7    9
  AMP PEAK 3(7P22.3) WILD-TYPE    9    6
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  CLUS_1                          7                            9
  CLUS_2                          9                            6
D3V8, multiclass

Clustering(4) Variable = Amp Peak 4(7q36.1) mutation analysis
D4V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(7Q36.1) MUTATED     10    8
  AMP PEAK 4(7Q36.1) WILD-TYPE    6    7
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                         10                            6
  CLUS_2                          8                            7
D4V2, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(7Q36.1) MUTATED      9    9
  AMP PEAK 4(7Q36.1) WILD-TYPE    5    8
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                          9                            5
  CLUS_2                          9                            8
D4V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(7Q36.1) MUTATED      4    7
  AMP PEAK 4(7Q36.1) WILD-TYPE    3    9
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                          4                            3
  CLUS_2                          7                            9
D4V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(7Q36.1) MUTATED      2    9
  AMP PEAK 4(7Q36.1) WILD-TYPE    2   10
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                          2                            2
  CLUS_2                          9                           10
D4V5, multiclass
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                          3                            5
  CLUS_2                          8                            3
  CLUS_3                          7                            5
D4V6, multiclass
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                          3                            3
  CLUS_2                          6                            2
  CLUS_3                          4                            3
  CLUS_4                          5                            5
D4V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(7Q36.1) MUTATED      9    9
  AMP PEAK 4(7Q36.1) WILD-TYPE    7    6
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  CLUS_1                          9                            7
  CLUS_2                          9                            6
D4V8, multiclass

Clustering(5) Variable = Amp Peak 5(12p12.1) mutation analysis
D5V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12P12.1) MUTATED      2    3
  AMP PEAK 5(12P12.1) WILD-TYPE   14   12
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           2                            14
  CLUS_2                           3                            12
D5V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12P12.1) MUTATED      4    1
  AMP PEAK 5(12P12.1) WILD-TYPE   10   16
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           1                            16
D5V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12P12.1) MUTATED      1    2
  AMP PEAK 5(12P12.1) WILD-TYPE    6   14
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           2                            14
D5V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12P12.1) MUTATED      1    2
  AMP PEAK 5(12P12.1) WILD-TYPE    3   17
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           1                             3
  CLUS_2                           2                            17
D5V5, multiclass
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           0                             8
  CLUS_2                           2                             9
  CLUS_3                           3                             9
D5V6, multiclass
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           1                             5
  CLUS_2                           1                             7
  CLUS_3                           1                             6
  CLUS_4                           2                             8
D5V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12P12.1) MUTATED      3    2
  AMP PEAK 5(12P12.1) WILD-TYPE   13   13
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  CLUS_1                           3                            13
  CLUS_2                           2                            13
D5V8, multiclass

Clustering(6) Variable = Amp Peak 6(15q26.2) mutation analysis
D6V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(15Q26.2) MUTATED      6    5
  AMP PEAK 6(15Q26.2) WILD-TYPE   10   10
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           6                            10
  CLUS_2                           5                            10
D6V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(15Q26.2) MUTATED      5    6
  AMP PEAK 6(15Q26.2) WILD-TYPE    9   11
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           5                             9
  CLUS_2                           6                            11
D6V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(15Q26.2) MUTATED      0    5
  AMP PEAK 6(15Q26.2) WILD-TYPE    7   11
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           0                             7
  CLUS_2                           5                            11
D6V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(15Q26.2) MUTATED      0    5
  AMP PEAK 6(15Q26.2) WILD-TYPE    4   14
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           5                            14
D6V5, multiclass
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           4                             4
  CLUS_2                           5                             6
  CLUS_3                           2                            10
D6V6, multiclass
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           2                             4
  CLUS_2                           4                             4
  CLUS_3                           1                             6
  CLUS_4                           4                             6
D6V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(15Q26.2) MUTATED      5    6
  AMP PEAK 6(15Q26.2) WILD-TYPE   11    9
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  CLUS_1                           5                            11
  CLUS_2                           6                             9
D6V8, multiclass

Clustering(7) Variable = Amp Peak 7(17q25.3) mutation analysis
D7V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.3) MUTATED      6   10
  AMP PEAK 7(17Q25.3) WILD-TYPE   10    5
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           6                            10
  CLUS_2                          10                             5
D7V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.3) MUTATED      8    8
  AMP PEAK 7(17Q25.3) WILD-TYPE    6    9
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           8                             6
  CLUS_2                           8                             9
D7V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.3) MUTATED      4    9
  AMP PEAK 7(17Q25.3) WILD-TYPE    3    7
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           4                             3
  CLUS_2                           9                             7
D7V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.3) MUTATED      3   10
  AMP PEAK 7(17Q25.3) WILD-TYPE    1    9
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           3                             1
  CLUS_2                          10                             9
D7V5, multiclass
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           2                             6
  CLUS_2                           6                             5
  CLUS_3                           8                             4
D7V6, multiclass
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           2                             4
  CLUS_2                           5                             3
  CLUS_3                           4                             3
  CLUS_4                           5                             5
D7V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.3) MUTATED      7    9
  AMP PEAK 7(17Q25.3) WILD-TYPE    9    6
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  CLUS_1                           7                             9
  CLUS_2                           9                             6
D7V8, multiclass

Clustering(8) Variable = Del Peak  1(1p36.31) mutation analysis
D8V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1    6
  DEL PEAK  1(1P36.31) WILD-TYPE   15    9
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            1                             15
  CLUS_2                            6                              9
D8V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      2    5
  DEL PEAK  1(1P36.31) WILD-TYPE   12   12
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            2                             12
  CLUS_2                            5                             12
D8V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1    2
  DEL PEAK  1(1P36.31) WILD-TYPE    6   14
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            2                             14
D8V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1    2
  DEL PEAK  1(1P36.31) WILD-TYPE    3   17
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            1                              3
  CLUS_2                            2                             17
D8V5, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            2                              6
  CLUS_2                            0                             11
  CLUS_3                            5                              7
D8V6, multiclass
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            0                              6
  CLUS_2                            0                              8
  CLUS_3                            3                              4
  CLUS_4                            4                              6
D8V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      4    3
  DEL PEAK  1(1P36.31) WILD-TYPE   12   12
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  CLUS_1                            4                             12
  CLUS_2                            3                             12
D8V8, multiclass

Clustering(9) Variable = Del Peak  2(1p13.2) mutation analysis
D9V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      3    6
  DEL PEAK  2(1P13.2) WILD-TYPE   13    9
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           3                            13
  CLUS_2                           6                             9
D9V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      3    6
  DEL PEAK  2(1P13.2) WILD-TYPE   11   11
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           3                            11
  CLUS_2                           6                            11
D9V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      1    5
  DEL PEAK  2(1P13.2) WILD-TYPE    6   11
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           5                            11
D9V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      0    6
  DEL PEAK  2(1P13.2) WILD-TYPE    4   13
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           6                            13
D9V5, multiclass
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           4                             4
  CLUS_2                           2                             9
  CLUS_3                           3                             9
D9V6, multiclass
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           2                             4
  CLUS_2                           2                             6
  CLUS_3                           2                             5
  CLUS_4                           3                             7
D9V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      5    4
  DEL PEAK  2(1P13.2) WILD-TYPE   11   11
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  CLUS_1                           5                            11
  CLUS_2                           4                            11
D9V8, multiclass

Clustering(10) Variable = Del Peak  3(2q37.3) mutation analysis
D10V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      5    5
  DEL PEAK  3(2Q37.3) WILD-TYPE   11   10
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           5                            11
  CLUS_2                           5                            10
D10V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      4    6
  DEL PEAK  3(2Q37.3) WILD-TYPE   10   11
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           4                            10
  CLUS_2                           6                            11
D10V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      1    6
  DEL PEAK  3(2Q37.3) WILD-TYPE    6   10
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           1                             6
  CLUS_2                           6                            10
D10V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      0    7
  DEL PEAK  3(2Q37.3) WILD-TYPE    4   12
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           0                             4
  CLUS_2                           7                            12
D10V5, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           2                             6
  CLUS_2                           3                             8
  CLUS_3                           5                             7
D10V6, multiclass
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           1                             5
  CLUS_2                           2                             6
  CLUS_3                           2                             5
  CLUS_4                           5                             5
D10V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      4    6
  DEL PEAK  3(2Q37.3) WILD-TYPE   12    9
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  CLUS_1                           4                            12
  CLUS_2                           6                             9
D10V8, multiclass

Clustering(11) Variable = Del Peak  4(3q23) mutation analysis
D11V1, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3Q23) MUTATED      2    2
  DEL PEAK  4(3Q23) WILD-TYPE   14   13
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         2                          14
  CLUS_2                         2                          13
D11V2, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3Q23) MUTATED      0    4
  DEL PEAK  4(3Q23) WILD-TYPE   14   13
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         0                          14
  CLUS_2                         4                          13
D11V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3Q23) MUTATED      0    3
  DEL PEAK  4(3Q23) WILD-TYPE    7   13
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         0                           7
  CLUS_2                         3                          13
D11V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3Q23) MUTATED      0    3
  DEL PEAK  4(3Q23) WILD-TYPE    4   16
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         0                           4
  CLUS_2                         3                          16
D11V5, multiclass
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         1                           7
  CLUS_2                         1                          10
  CLUS_3                         2                          10
D11V6, multiclass
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         0                           6
  CLUS_2                         1                           7
  CLUS_3                         1                           6
  CLUS_4                         2                           8
D11V7, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3Q23) MUTATED      2    2
  DEL PEAK  4(3Q23) WILD-TYPE   14   13
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  CLUS_1                         2                          14
  CLUS_2                         2                          13
D11V8, multiclass

Clustering(12) Variable = Del Peak  5(6q23.2) mutation analysis
D12V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.2) MUTATED      3   11
  DEL PEAK  5(6Q23.2) WILD-TYPE   13    4
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           3                            13
  CLUS_2                          11                             4
D12V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.2) MUTATED      5    9
  DEL PEAK  5(6Q23.2) WILD-TYPE    9    8
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           5                             9
  CLUS_2                           9                             8
D12V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.2) MUTATED      5    6
  DEL PEAK  5(6Q23.2) WILD-TYPE    2   10
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           5                             2
  CLUS_2                           6                            10
D12V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.2) MUTATED      3    8
  DEL PEAK  5(6Q23.2) WILD-TYPE    1   11
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           3                             1
  CLUS_2                           8                            11
D12V5, multiclass
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           3                             5
  CLUS_2                           3                             8
  CLUS_3                           8                             4
D12V6, multiclass
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           2                             4
  CLUS_2                           2                             6
  CLUS_3                           4                             3
  CLUS_4                           6                             4
D12V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.2) MUTATED      6    8
  DEL PEAK  5(6Q23.2) WILD-TYPE   10    7
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  CLUS_1                           6                            10
  CLUS_2                           8                             7
D12V8, multiclass

Clustering(13) Variable = Del Peak  6(9p21.3) mutation analysis
D13V1, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      8   12
  DEL PEAK  6(9P21.3) WILD-TYPE    8    3
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           8                             8
  CLUS_2                          12                             3
D13V2, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      7   13
  DEL PEAK  6(9P21.3) WILD-TYPE    7    4
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           7                             7
  CLUS_2                          13                             4
D13V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      5   12
  DEL PEAK  6(9P21.3) WILD-TYPE    2    4
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           5                             2
  CLUS_2                          12                             4
D13V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      3   14
  DEL PEAK  6(9P21.3) WILD-TYPE    1    5
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           3                             1
  CLUS_2                          14                             5
D13V5, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           6                             2
  CLUS_2                           6                             5
  CLUS_3                           8                             4
D13V6, multiclass
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                           4                             2
  CLUS_2                           4                             4
  CLUS_3                           5                             2
  CLUS_4                           7                             3
D13V7, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED     11    9
  DEL PEAK  6(9P21.3) WILD-TYPE    5    6
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  CLUS_1                          11                             5
  CLUS_2                           9                             6
D13V8, multiclass

Clustering(14) Variable = Del Peak  7(10p15.1) mutation analysis
D14V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(10P15.1) MUTATED      6    7
  DEL PEAK  7(10P15.1) WILD-TYPE   10    8
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            6                             10
  CLUS_2                            7                              8
D14V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(10P15.1) MUTATED      6    7
  DEL PEAK  7(10P15.1) WILD-TYPE    8   10
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            6                              8
  CLUS_2                            7                             10
D14V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(10P15.1) MUTATED      1    9
  DEL PEAK  7(10P15.1) WILD-TYPE    6    7
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            1                              6
  CLUS_2                            9                              7
D14V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(10P15.1) MUTATED      0   10
  DEL PEAK  7(10P15.1) WILD-TYPE    4    9
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                           10                              9
D14V5, multiclass
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            6                              2
  CLUS_2                            5                              6
  CLUS_3                            2                             10
D14V6, multiclass
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            4                              2
  CLUS_2                            4                              4
  CLUS_3                            0                              7
  CLUS_4                            5                              5
D14V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(10P15.1) MUTATED      6    7
  DEL PEAK  7(10P15.1) WILD-TYPE   10    8
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  CLUS_1                            6                             10
  CLUS_2                            7                              8
D14V8, multiclass

Clustering(15) Variable = Del Peak  8(10q24.33) mutation analysis
D15V1, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  8(10Q24.33) MUTATED      7    7
  DEL PEAK  8(10Q24.33) WILD-TYPE    9    8
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             7                               9
  CLUS_2                             7                               8
D15V2, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  8(10Q24.33) MUTATED      5    9
  DEL PEAK  8(10Q24.33) WILD-TYPE    9    8
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             5                               9
  CLUS_2                             9                               8
D15V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  8(10Q24.33) MUTATED      1    9
  DEL PEAK  8(10Q24.33) WILD-TYPE    6    7
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             1                               6
  CLUS_2                             9                               7
D15V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  8(10Q24.33) MUTATED      0   10
  DEL PEAK  8(10Q24.33) WILD-TYPE    4    9
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             0                               4
  CLUS_2                            10                               9
D15V5, multiclass
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             5                               3
  CLUS_2                             6                               5
  CLUS_3                             3                               9
D15V6, multiclass
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             4                               2
  CLUS_2                             5                               3
  CLUS_3                             1                               6
  CLUS_4                             4                               6
D15V7, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  8(10Q24.33) MUTATED      7    7
  DEL PEAK  8(10Q24.33) WILD-TYPE    9    8
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  CLUS_1                             7                               9
  CLUS_2                             7                               8
D15V8, multiclass

Clustering(16) Variable = Del Peak  9(11q24.3) mutation analysis
D16V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q24.3) MUTATED      9   12
  DEL PEAK  9(11Q24.3) WILD-TYPE    7    3
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                            9                              7
  CLUS_2                           12                              3
D16V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q24.3) MUTATED      9   12
  DEL PEAK  9(11Q24.3) WILD-TYPE    5    5
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                            9                              5
  CLUS_2                           12                              5
D16V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q24.3) MUTATED      5   13
  DEL PEAK  9(11Q24.3) WILD-TYPE    2    3
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                            5                              2
  CLUS_2                           13                              3
D16V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q24.3) MUTATED      2   16
  DEL PEAK  9(11Q24.3) WILD-TYPE    2    3
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                            2                              2
  CLUS_2                           16                              3
D16V5, multiclass
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                            5                              3
  CLUS_2                            8                              3
  CLUS_3                            8                              4
D16V6, multiclass
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                            4                              2
  CLUS_2                            6                              2
  CLUS_3                            3                              4
  CLUS_4                            8                              2
D16V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q24.3) MUTATED     10   11
  DEL PEAK  9(11Q24.3) WILD-TYPE    6    4
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  CLUS_1                           10                              6
  CLUS_2                           11                              4
D16V8, multiclass

Clustering(17) Variable = Del Peak 10(13q34) mutation analysis
D17V1, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(13Q34) MUTATED      5    3
  DEL PEAK 10(13Q34) WILD-TYPE   11   12
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          5                           11
  CLUS_2                          3                           12
D17V2, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(13Q34) MUTATED      5    3
  DEL PEAK 10(13Q34) WILD-TYPE    9   14
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          5                            9
  CLUS_2                          3                           14
D17V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(13Q34) MUTATED      3    4
  DEL PEAK 10(13Q34) WILD-TYPE    4   12
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          3                            4
  CLUS_2                          4                           12
D17V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(13Q34) MUTATED      1    6
  DEL PEAK 10(13Q34) WILD-TYPE    3   13
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          1                            3
  CLUS_2                          6                           13
D17V5, multiclass
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          2                            6
  CLUS_2                          5                            6
  CLUS_3                          1                           11
D17V6, multiclass
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          2                            4
  CLUS_2                          4                            4
  CLUS_3                          1                            6
  CLUS_4                          1                            9
D17V7, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(13Q34) MUTATED      4    4
  DEL PEAK 10(13Q34) WILD-TYPE   12   11
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  CLUS_1                          4                           12
  CLUS_2                          4                           11
D17V8, multiclass

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

Clustering(19) Variable = Del Peak 12(16q12.1) mutation analysis
D19V1, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q12.1) MUTATED      9    5
  DEL PEAK 12(16Q12.1) WILD-TYPE    7   10
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            9                              7
  CLUS_2                            5                             10
D19V2, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q12.1) MUTATED      6    8
  DEL PEAK 12(16Q12.1) WILD-TYPE    8    9
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            6                              8
  CLUS_2                            8                              9
D19V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q12.1) MUTATED      2    8
  DEL PEAK 12(16Q12.1) WILD-TYPE    5    8
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            2                              5
  CLUS_2                            8                              8
D19V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q12.1) MUTATED      0   10
  DEL PEAK 12(16Q12.1) WILD-TYPE    4    9
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            0                              4
  CLUS_2                           10                              9
D19V5, multiclass
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            4                              4
  CLUS_2                            8                              3
  CLUS_3                            2                             10
D19V6, multiclass
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            2                              4
  CLUS_2                            7                              1
  CLUS_3                            1                              6
  CLUS_4                            4                              6
D19V7, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q12.1) MUTATED      7    7
  DEL PEAK 12(16Q12.1) WILD-TYPE    9    8
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  CLUS_1                            7                              9
  CLUS_2                            7                              8
D19V8, multiclass
                     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")
