
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/375888/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LAML-TB/2907506/1.GDAC_mergedClustering.Finished/LAML-TB.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LAML-TB", "-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=LAML-TB"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=200, in cluster file=191, common to both=191
[1] "Reduce the number of clustering variables from 22 to 20."
[1]  20 191
[1] "Amp Peak 1(1p33) mutation analysis"
[1] 3
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         7                        184 
  AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE 
                         7                        184 
[1] "Amp Peak 2(1q43) mutation analysis"
[1] 3
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         7                        184 
  AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE 
                         7                        184 
[1] "Amp Peak 3(11q23.3) mutation analysis"
[1] 3
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                           17                           174 
  AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE 
                           17                           174 
[1] "Amp Peak 4(13q31.3) mutation analysis"
[1] 3
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            7                           184 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            7                           184 
[1] "Amp Peak 5(20q11.21) mutation analysis"
[1] 3
  AMP PEAK 5(20Q11.21) MUTATED AMP PEAK 5(20Q11.21) WILD-TYPE 
                             3                            188 
  AMP PEAK 5(20Q11.21) MUTATED AMP PEAK 5(20Q11.21) WILD-TYPE 
                             3                            188 
[1] "Amp Peak 6(21q22.2) mutation analysis"
[1] 3
  AMP PEAK 6(21Q22.2) MUTATED AMP PEAK 6(21Q22.2) WILD-TYPE 
                           14                           177 
  AMP PEAK 6(21Q22.2) MUTATED AMP PEAK 6(21Q22.2) WILD-TYPE 
                           14                           177 
[1] "Del Peak  2(3p13) mutation analysis"
[1] 3
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          9                         182 
  DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE 
                          9                         182 
[1] "Del Peak  3(3q26.31) mutation analysis"
[1] 3
  DEL PEAK  3(3Q26.31) MUTATED DEL PEAK  3(3Q26.31) WILD-TYPE 
                             3                            188 
  DEL PEAK  3(3Q26.31) MUTATED DEL PEAK  3(3Q26.31) WILD-TYPE 
                             3                            188 
[1] "Del Peak  4(5q31.2) mutation analysis"
[1] 3
  DEL PEAK  4(5Q31.2) MUTATED DEL PEAK  4(5Q31.2) WILD-TYPE 
                           18                           173 
  DEL PEAK  4(5Q31.2) MUTATED DEL PEAK  4(5Q31.2) WILD-TYPE 
                           18                           173 
[1] "Del Peak  5(7p12.1) mutation analysis"
[1] 3
  DEL PEAK  5(7P12.1) MUTATED DEL PEAK  5(7P12.1) WILD-TYPE 
                           16                           175 
  DEL PEAK  5(7P12.1) MUTATED DEL PEAK  5(7P12.1) WILD-TYPE 
                           16                           175 
[1] "Del Peak  6(7q32.3) mutation analysis"
[1] 3
  DEL PEAK  6(7Q32.3) MUTATED DEL PEAK  6(7Q32.3) WILD-TYPE 
                           23                           168 
  DEL PEAK  6(7Q32.3) MUTATED DEL PEAK  6(7Q32.3) WILD-TYPE 
                           23                           168 
[1] "Del Peak  7(7q34) mutation analysis"
[1] 3
  DEL PEAK  7(7Q34) MUTATED DEL PEAK  7(7Q34) WILD-TYPE 
                         24                         167 
  DEL PEAK  7(7Q34) MUTATED DEL PEAK  7(7Q34) WILD-TYPE 
                         24                         167 
[1] "Del Peak  9(9q21.32) mutation analysis"
[1] 3
  DEL PEAK  9(9Q21.32) MUTATED DEL PEAK  9(9Q21.32) WILD-TYPE 
                             5                            186 
  DEL PEAK  9(9Q21.32) MUTATED DEL PEAK  9(9Q21.32) WILD-TYPE 
                             5                            186 
[1] "Del Peak 10(12p13.2) mutation analysis"
[1] 3
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                            10                            181 
  DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE 
                            10                            181 
[1] "Del Peak 11(12q21.33) mutation analysis"
[1] 3
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              3                             188 
  DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE 
                              3                             188 
[1] "Del Peak 12(16q23.1) mutation analysis"
[1] 3
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             9                            182 
  DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE 
                             9                            182 
[1] "Del Peak 13(17p13.2) mutation analysis"
[1] 3
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                            15                            176 
  DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE 
                            15                            176 
[1] "Del Peak 14(17q11.2) mutation analysis"
[1] 3
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                            13                            178 
  DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE 
                            13                            178 
[1] "Del Peak 15(18p11.21) mutation analysis"
[1] 3
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                              9                             182 
  DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE 
                              9                             182 
[1] "Del Peak 16(20q13.13) mutation analysis"
[1] 3
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              4                             187 
  DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE 
                              4                             187 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 191 columns.

Variable 1:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 191 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(1p33) mutation analysis
D1V1, multiclass
D1V2, multiclass
D1V3, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        5                         65
  CLUS_2                        1                         51
  CLUS_3                        0                         44
D1V4, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P33) MUTATED      5    1
  AMP PEAK 1(1P33) WILD-TYPE  105   55
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        1                         55
  CLUS_2                        5                        105
D1V5, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        4                         79
  CLUS_2                        3                         35
  CLUS_3                        0                         57
D1V6, multiclass
        clus
vv       AMP PEAK 1(1P33) MUTATED AMP PEAK 1(1P33) WILD-TYPE
  CLUS_1                        3                         34
  CLUS_2                        3                         76
  CLUS_3                        1                         61

Clustering(2) Variable = Amp Peak 2(1q43) mutation analysis
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
        clus
vv       AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  CLUS_1                        5                         65
  CLUS_2                        1                         51
  CLUS_3                        1                         43
D2V4, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q43) MUTATED      6    1
  AMP PEAK 2(1Q43) WILD-TYPE  104   55
        clus
vv       AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  CLUS_1                        1                         55
  CLUS_2                        6                        104
D2V5, multiclass
        clus
vv       AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  CLUS_1                        2                         81
  CLUS_2                        3                         35
  CLUS_3                        2                         55
D2V6, multiclass
        clus
vv       AMP PEAK 2(1Q43) MUTATED AMP PEAK 2(1Q43) WILD-TYPE
  CLUS_1                        3                         34
  CLUS_2                        1                         78
  CLUS_3                        3                         59

Clustering(3) Variable = Amp Peak 3(11q23.3) mutation analysis
D3V1, multiclass
D3V2, multiclass
D3V3, multiclass
        clus
vv       AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE
  CLUS_1                           9                            61
  CLUS_2                           5                            47
  CLUS_3                           2                            42
D3V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(11Q23.3) MUTATED     10    6
  AMP PEAK 3(11Q23.3) WILD-TYPE  100   50
        clus
vv       AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE
  CLUS_1                           6                            50
  CLUS_2                          10                           100
D3V5, multiclass
        clus
vv       AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE
  CLUS_1                           8                            75
  CLUS_2                           4                            34
  CLUS_3                           5                            52
D3V6, multiclass
        clus
vv       AMP PEAK 3(11Q23.3) MUTATED AMP PEAK 3(11Q23.3) WILD-TYPE
  CLUS_1                           3                            34
  CLUS_2                           7                            72
  CLUS_3                           7                            55

Clustering(4) Variable = Amp Peak 4(13q31.3) mutation analysis
D4V1, multiclass
D4V2, multiclass
D4V3, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           6                            64
  CLUS_2                           1                            51
  CLUS_3                           0                            44
D4V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(13Q31.3) MUTATED      7    0
  AMP PEAK 4(13Q31.3) WILD-TYPE  103   56
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           0                            56
  CLUS_2                           7                           103
D4V5, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           4                            79
  CLUS_2                           2                            36
  CLUS_3                           1                            56
D4V6, multiclass
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  CLUS_1                           2                            35
  CLUS_2                           1                            78
  CLUS_3                           4                            58

Clustering(5) Variable = Amp Peak 5(20q11.21) mutation analysis
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 5(20Q11.21) MUTATED"
clus
  AMP PEAK 5(20Q11.21) MUTATED AMP PEAK 5(20Q11.21) WILD-TYPE 
                             2                            164 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2879                     TCGA-AB-2880 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2881                     TCGA-AB-2882 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2895 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2896                     TCGA-AB-2897 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2898                     TCGA-AB-2899 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2900                     TCGA-AB-2901 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2903                     TCGA-AB-2908 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2909                     TCGA-AB-2910 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2911                     TCGA-AB-2912 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2913                     TCGA-AB-2914 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2915                     TCGA-AB-2916 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2917                     TCGA-AB-2919 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2920                     TCGA-AB-2921 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2924                     TCGA-AB-2925 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2927                     TCGA-AB-2928 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2929                     TCGA-AB-2930 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2931                     TCGA-AB-2932 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2933                     TCGA-AB-2934 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2935                     TCGA-AB-2936 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2937                     TCGA-AB-2938 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2939                     TCGA-AB-2940 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2941                     TCGA-AB-2942 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2943                     TCGA-AB-2944 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2946                     TCGA-AB-2948 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2949                     TCGA-AB-2950 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2952                     TCGA-AB-2954 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2955                     TCGA-AB-2956 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2959                     TCGA-AB-2963 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2964                     TCGA-AB-2965 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2966                     TCGA-AB-2967 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2969                     TCGA-AB-2970 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2971                     TCGA-AB-2972 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2973                     TCGA-AB-2975 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2976                     TCGA-AB-2977 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2978                     TCGA-AB-2980 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2982                     TCGA-AB-2983 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2984                     TCGA-AB-2985 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2986                     TCGA-AB-2987 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2988                     TCGA-AB-2990 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2991                     TCGA-AB-2992 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2993                     TCGA-AB-2994 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2995                     TCGA-AB-2996 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2998                     TCGA-AB-2999 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3000                     TCGA-AB-3001 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3002                     TCGA-AB-3005 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3006                     TCGA-AB-3007 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3008                     TCGA-AB-3009 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3011                     TCGA-AB-3012 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
D5V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 5(20Q11.21) MUTATED      2    0
  AMP PEAK 5(20Q11.21) WILD-TYPE  108   56
        clus
vv       AMP PEAK 5(20Q11.21) MUTATED AMP PEAK 5(20Q11.21) WILD-TYPE
  CLUS_1                            0                             56
  CLUS_2                            2                            108
D5V5, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 5(20Q11.21) MUTATED"
clus
  AMP PEAK 5(20Q11.21) MUTATED AMP PEAK 5(20Q11.21) WILD-TYPE 
                             2                            176 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2878                     TCGA-AB-2879 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2880                     TCGA-AB-2881 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2882                     TCGA-AB-2883 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2892 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2893                     TCGA-AB-2894 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2895                     TCGA-AB-2897 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2898                     TCGA-AB-2899 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2900                     TCGA-AB-2901 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2903                     TCGA-AB-2908 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2909                     TCGA-AB-2910 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2911                     TCGA-AB-2912 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2913                     TCGA-AB-2914 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2915                     TCGA-AB-2916 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2917                     TCGA-AB-2919 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2920                     TCGA-AB-2921 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2922                     TCGA-AB-2923 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2924                     TCGA-AB-2925 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2926                     TCGA-AB-2927 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2928                     TCGA-AB-2929 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2930                     TCGA-AB-2931 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2932                     TCGA-AB-2933 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2934                     TCGA-AB-2935 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2936                     TCGA-AB-2937 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2938                     TCGA-AB-2939 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2940                     TCGA-AB-2941 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2942                     TCGA-AB-2943 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2944                     TCGA-AB-2945 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2946                     TCGA-AB-2947 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2948                     TCGA-AB-2949 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2950                     TCGA-AB-2952 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2954                     TCGA-AB-2955 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2956                     TCGA-AB-2957 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2959                     TCGA-AB-2963 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2964                     TCGA-AB-2965 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2966                     TCGA-AB-2967 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2969                     TCGA-AB-2970 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2971                     TCGA-AB-2972 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2973                     TCGA-AB-2975 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2976                     TCGA-AB-2977 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2978                     TCGA-AB-2980 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2982                     TCGA-AB-2983 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2984                     TCGA-AB-2985 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2986                     TCGA-AB-2987 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2988                     TCGA-AB-2989 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2990                     TCGA-AB-2991 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2992                     TCGA-AB-2993 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2994                     TCGA-AB-2995 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2996                     TCGA-AB-2997 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2998                     TCGA-AB-2999 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3000                     TCGA-AB-3001 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3002                     TCGA-AB-3005 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3006                     TCGA-AB-3007 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3008                     TCGA-AB-3009 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3011                     TCGA-AB-3012 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
D5V6, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 5(20Q11.21) MUTATED"
clus
  AMP PEAK 5(20Q11.21) MUTATED AMP PEAK 5(20Q11.21) WILD-TYPE 
                             2                            176 
                    TCGA-AB-2803                     TCGA-AB-2805 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2806                     TCGA-AB-2807 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2808                     TCGA-AB-2810 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2811                     TCGA-AB-2812 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2813                     TCGA-AB-2814 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2815                     TCGA-AB-2816 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2817                     TCGA-AB-2818 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2819                     TCGA-AB-2820 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2821                     TCGA-AB-2822 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2823                     TCGA-AB-2824 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2825                     TCGA-AB-2826 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2828                     TCGA-AB-2830 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2832                     TCGA-AB-2834 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2835                     TCGA-AB-2836 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2837                     TCGA-AB-2838 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2839                     TCGA-AB-2840 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2841                     TCGA-AB-2842 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2844                     TCGA-AB-2845 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2846                     TCGA-AB-2848 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2849                     TCGA-AB-2851 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2853                     TCGA-AB-2854 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2855                     TCGA-AB-2856 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2857                     TCGA-AB-2858 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2859                     TCGA-AB-2860 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2861                     TCGA-AB-2862 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2863                     TCGA-AB-2865 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2866                     TCGA-AB-2867 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2869                     TCGA-AB-2870 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2871                     TCGA-AB-2872 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2873                     TCGA-AB-2874 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2875                     TCGA-AB-2877 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2878                     TCGA-AB-2879 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2880                     TCGA-AB-2881 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2882                     TCGA-AB-2883 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2884                     TCGA-AB-2885 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2886                     TCGA-AB-2887 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2888                     TCGA-AB-2889 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2890                     TCGA-AB-2892 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2893                     TCGA-AB-2894 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2895                     TCGA-AB-2897 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2898                     TCGA-AB-2899 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2900                     TCGA-AB-2901 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2903                     TCGA-AB-2908 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2909                     TCGA-AB-2910 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2911                     TCGA-AB-2912 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2913                     TCGA-AB-2914 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2915                     TCGA-AB-2916 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2917                     TCGA-AB-2919 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2920                     TCGA-AB-2921 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2922                     TCGA-AB-2923 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2924                     TCGA-AB-2925 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2926                     TCGA-AB-2927 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2928                     TCGA-AB-2929 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2930                     TCGA-AB-2931 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2932                     TCGA-AB-2933 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2934                     TCGA-AB-2935 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2936                     TCGA-AB-2937 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2938                     TCGA-AB-2939 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2940                     TCGA-AB-2941 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2942                     TCGA-AB-2943 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2944                     TCGA-AB-2945 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2946                     TCGA-AB-2947 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2948                     TCGA-AB-2949 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2950                     TCGA-AB-2952 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2954                     TCGA-AB-2955 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2956                     TCGA-AB-2957 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2959                     TCGA-AB-2963 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2964                     TCGA-AB-2965 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2966                     TCGA-AB-2967 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2969                     TCGA-AB-2970 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2971                     TCGA-AB-2972 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2973                     TCGA-AB-2975 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2976                     TCGA-AB-2977 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2978                     TCGA-AB-2980 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2982                     TCGA-AB-2983 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2984                     TCGA-AB-2985 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2986                     TCGA-AB-2987 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2988                     TCGA-AB-2989 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2990                     TCGA-AB-2991 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2992                     TCGA-AB-2993 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2994                     TCGA-AB-2995 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2996                     TCGA-AB-2997 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-2998                     TCGA-AB-2999 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3000                     TCGA-AB-3001 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3002                     TCGA-AB-3005 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3006                     TCGA-AB-3007 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3008                     TCGA-AB-3009 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 
                    TCGA-AB-3011                     TCGA-AB-3012 
"AMP PEAK 5(20Q11.21) WILD-TYPE" "AMP PEAK 5(20Q11.21) WILD-TYPE" 

Clustering(6) Variable = Amp Peak 6(21q22.2) mutation analysis
D6V1, multiclass
D6V2, multiclass
D6V3, multiclass
        clus
vv       AMP PEAK 6(21Q22.2) MUTATED AMP PEAK 6(21Q22.2) WILD-TYPE
  CLUS_1                          10                            60
  CLUS_2                           1                            51
  CLUS_3                           0                            44
D6V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(21Q22.2) MUTATED      9    2
  AMP PEAK 6(21Q22.2) WILD-TYPE  101   54
        clus
vv       AMP PEAK 6(21Q22.2) MUTATED AMP PEAK 6(21Q22.2) WILD-TYPE
  CLUS_1                           2                            54
  CLUS_2                           9                           101
D6V5, multiclass
        clus
vv       AMP PEAK 6(21Q22.2) MUTATED AMP PEAK 6(21Q22.2) WILD-TYPE
  CLUS_1                           1                            82
  CLUS_2                           4                            34
  CLUS_3                           7                            50
D6V6, multiclass
        clus
vv       AMP PEAK 6(21Q22.2) MUTATED AMP PEAK 6(21Q22.2) WILD-TYPE
  CLUS_1                           4                            33
  CLUS_2                           1                            78
  CLUS_3                           7                            55

Clustering(7) Variable = Del Peak  2(3p13) mutation analysis
D7V1, multiclass
D7V2, multiclass
D7V3, multiclass
        clus
vv       DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE
  CLUS_1                         7                          63
  CLUS_2                         1                          51
  CLUS_3                         0                          44
D7V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(3P13) MUTATED      6    2
  DEL PEAK  2(3P13) WILD-TYPE  104   54
        clus
vv       DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE
  CLUS_1                         2                          54
  CLUS_2                         6                         104
D7V5, multiclass
        clus
vv       DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE
  CLUS_1                         0                          83
  CLUS_2                         5                          33
  CLUS_3                         3                          54
D7V6, multiclass
        clus
vv       DEL PEAK  2(3P13) MUTATED DEL PEAK  2(3P13) WILD-TYPE
  CLUS_1                         5                          32
  CLUS_2                         0                          79
  CLUS_3                         3                          59

Clustering(8) Variable = Del Peak  3(3q26.31) mutation analysis
D8V1, multiclass
D8V2, multiclass
D8V3, multiclass
        clus
vv       DEL PEAK  3(3Q26.31) MUTATED DEL PEAK  3(3Q26.31) WILD-TYPE
  CLUS_1                            2                             68
  CLUS_2                            1                             51
  CLUS_3                            0                             44
D8V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  3(3Q26.31) MUTATED      2    1
  DEL PEAK  3(3Q26.31) WILD-TYPE  108   55
        clus
vv       DEL PEAK  3(3Q26.31) MUTATED DEL PEAK  3(3Q26.31) WILD-TYPE
  CLUS_1                            1                             55
  CLUS_2                            2                            108
D8V5, multiclass
        clus
vv       DEL PEAK  3(3Q26.31) MUTATED DEL PEAK  3(3Q26.31) WILD-TYPE
  CLUS_1                            0                             83
  CLUS_2                            2                             36
  CLUS_3                            1                             56
D8V6, multiclass
        clus
vv       DEL PEAK  3(3Q26.31) MUTATED DEL PEAK  3(3Q26.31) WILD-TYPE
  CLUS_1                            2                             35
  CLUS_2                            0                             79
  CLUS_3                            1                             61

Clustering(9) Variable = Del Peak  4(5q31.2) mutation analysis
D9V1, multiclass
D9V2, multiclass
D9V3, multiclass
        clus
vv       DEL PEAK  4(5Q31.2) MUTATED DEL PEAK  4(5Q31.2) WILD-TYPE
  CLUS_1                          13                            57
  CLUS_2                           2                            50
  CLUS_3                           1                            43
D9V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(5Q31.2) MUTATED     14    2
  DEL PEAK  4(5Q31.2) WILD-TYPE   96   54
        clus
vv       DEL PEAK  4(5Q31.2) MUTATED DEL PEAK  4(5Q31.2) WILD-TYPE
  CLUS_1                           2                            54
  CLUS_2                          14                            96
D9V5, multiclass
        clus
vv       DEL PEAK  4(5Q31.2) MUTATED DEL PEAK  4(5Q31.2) WILD-TYPE
  CLUS_1                           4                            79
  CLUS_2                          10                            28
  CLUS_3                           3                            54
D9V6, multiclass
        clus
vv       DEL PEAK  4(5Q31.2) MUTATED DEL PEAK  4(5Q31.2) WILD-TYPE
  CLUS_1                          10                            27
  CLUS_2                           3                            76
  CLUS_3                           4                            58

Clustering(10) Variable = Del Peak  5(7p12.1) mutation analysis
D10V1, multiclass
D10V2, multiclass
D10V3, multiclass
        clus
vv       DEL PEAK  5(7P12.1) MUTATED DEL PEAK  5(7P12.1) WILD-TYPE
  CLUS_1                          12                            58
  CLUS_2                           0                            52
  CLUS_3                           3                            41
D10V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7P12.1) MUTATED     15    0
  DEL PEAK  5(7P12.1) WILD-TYPE   95   56
        clus
vv       DEL PEAK  5(7P12.1) MUTATED DEL PEAK  5(7P12.1) WILD-TYPE
  CLUS_1                           0                            56
  CLUS_2                          15                            95
D10V5, multiclass
        clus
vv       DEL PEAK  5(7P12.1) MUTATED DEL PEAK  5(7P12.1) WILD-TYPE
  CLUS_1                           4                            79
  CLUS_2                           9                            29
  CLUS_3                           3                            54
D10V6, multiclass
        clus
vv       DEL PEAK  5(7P12.1) MUTATED DEL PEAK  5(7P12.1) WILD-TYPE
  CLUS_1                           9                            28
  CLUS_2                           4                            75
  CLUS_3                           3                            59

Clustering(11) Variable = Del Peak  6(7q32.3) mutation analysis
D11V1, multiclass
D11V2, multiclass
D11V3, multiclass
        clus
vv       DEL PEAK  6(7Q32.3) MUTATED DEL PEAK  6(7Q32.3) WILD-TYPE
  CLUS_1                          13                            57
  CLUS_2                           2                            50
  CLUS_3                           4                            40
D11V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(7Q32.3) MUTATED     17    2
  DEL PEAK  6(7Q32.3) WILD-TYPE   93   54
        clus
vv       DEL PEAK  6(7Q32.3) MUTATED DEL PEAK  6(7Q32.3) WILD-TYPE
  CLUS_1                           2                            54
  CLUS_2                          17                            93
D11V5, multiclass
        clus
vv       DEL PEAK  6(7Q32.3) MUTATED DEL PEAK  6(7Q32.3) WILD-TYPE
  CLUS_1                           4                            79
  CLUS_2                          12                            26
  CLUS_3                           6                            51
D11V6, multiclass
        clus
vv       DEL PEAK  6(7Q32.3) MUTATED DEL PEAK  6(7Q32.3) WILD-TYPE
  CLUS_1                          12                            25
  CLUS_2                           4                            75
  CLUS_3                           6                            56

Clustering(12) Variable = Del Peak  7(7q34) mutation analysis
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       DEL PEAK  7(7Q34) MUTATED DEL PEAK  7(7Q34) WILD-TYPE
  CLUS_1                        14                          56
  CLUS_2                         2                          50
  CLUS_3                         4                          40
D12V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(7Q34) MUTATED     18    2
  DEL PEAK  7(7Q34) WILD-TYPE   92   54
        clus
vv       DEL PEAK  7(7Q34) MUTATED DEL PEAK  7(7Q34) WILD-TYPE
  CLUS_1                         2                          54
  CLUS_2                        18                          92
D12V5, multiclass
        clus
vv       DEL PEAK  7(7Q34) MUTATED DEL PEAK  7(7Q34) WILD-TYPE
  CLUS_1                         4                          79
  CLUS_2                        13                          25
  CLUS_3                         6                          51
D12V6, multiclass
        clus
vv       DEL PEAK  7(7Q34) MUTATED DEL PEAK  7(7Q34) WILD-TYPE
  CLUS_1                        13                          24
  CLUS_2                         4                          75
  CLUS_3                         6                          56

Clustering(13) Variable = Del Peak  9(9q21.32) mutation analysis
D13V1, multiclass
D13V2, multiclass
D13V3, multiclass
        clus
vv       DEL PEAK  9(9Q21.32) MUTATED DEL PEAK  9(9Q21.32) WILD-TYPE
  CLUS_1                            4                             66
  CLUS_2                            0                             52
  CLUS_3                            1                             43
D13V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(9Q21.32) MUTATED      4    1
  DEL PEAK  9(9Q21.32) WILD-TYPE  106   55
        clus
vv       DEL PEAK  9(9Q21.32) MUTATED DEL PEAK  9(9Q21.32) WILD-TYPE
  CLUS_1                            1                             55
  CLUS_2                            4                            106
D13V5, multiclass
        clus
vv       DEL PEAK  9(9Q21.32) MUTATED DEL PEAK  9(9Q21.32) WILD-TYPE
  CLUS_1                            1                             82
  CLUS_2                            3                             35
  CLUS_3                            1                             56
D13V6, multiclass
        clus
vv       DEL PEAK  9(9Q21.32) MUTATED DEL PEAK  9(9Q21.32) WILD-TYPE
  CLUS_1                            3                             34
  CLUS_2                            1                             78
  CLUS_3                            1                             61

Clustering(14) Variable = Del Peak 10(12p13.2) mutation analysis
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE
  CLUS_1                            7                             63
  CLUS_2                            1                             51
  CLUS_3                            2                             42
D14V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(12P13.2) MUTATED      9    1
  DEL PEAK 10(12P13.2) WILD-TYPE  101   55
        clus
vv       DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE
  CLUS_1                            1                             55
  CLUS_2                            9                            101
D14V5, multiclass
        clus
vv       DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE
  CLUS_1                            3                             80
  CLUS_2                            5                             33
  CLUS_3                            2                             55
D14V6, multiclass
        clus
vv       DEL PEAK 10(12P13.2) MUTATED DEL PEAK 10(12P13.2) WILD-TYPE
  CLUS_1                            5                             32
  CLUS_2                            1                             78
  CLUS_3                            4                             58

Clustering(15) Variable = Del Peak 11(12q21.33) mutation analysis
D15V1, multiclass
D15V2, multiclass
D15V3, multiclass
        clus
vv       DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE
  CLUS_1                             3                              67
  CLUS_2                             0                              52
  CLUS_3                             0                              44
D15V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(12Q21.33) MUTATED      3    0
  DEL PEAK 11(12Q21.33) WILD-TYPE  107   56
        clus
vv       DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE
  CLUS_1                             0                              56
  CLUS_2                             3                             107
D15V5, multiclass
        clus
vv       DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE
  CLUS_1                             0                              83
  CLUS_2                             3                              35
  CLUS_3                             0                              57
D15V6, multiclass
        clus
vv       DEL PEAK 11(12Q21.33) MUTATED DEL PEAK 11(12Q21.33) WILD-TYPE
  CLUS_1                             3                              34
  CLUS_2                             0                              79
  CLUS_3                             0                              62

Clustering(16) Variable = Del Peak 12(16q23.1) mutation analysis
D16V1, multiclass
D16V2, multiclass
D16V3, multiclass
        clus
vv       DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE
  CLUS_1                            4                             66
  CLUS_2                            2                             50
  CLUS_3                            0                             44
D16V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q23.1) MUTATED      4    2
  DEL PEAK 12(16Q23.1) WILD-TYPE  106   54
        clus
vv       DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE
  CLUS_1                            2                             54
  CLUS_2                            4                            106
D16V5, multiclass
        clus
vv       DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE
  CLUS_1                            1                             82
  CLUS_2                            4                             34
  CLUS_3                            3                             54
D16V6, multiclass
        clus
vv       DEL PEAK 12(16Q23.1) MUTATED DEL PEAK 12(16Q23.1) WILD-TYPE
  CLUS_1                            4                             33
  CLUS_2                            1                             78
  CLUS_3                            3                             59

Clustering(17) Variable = Del Peak 13(17p13.2) mutation analysis
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE
  CLUS_1                           12                             58
  CLUS_2                            2                             50
  CLUS_3                            1                             43
D17V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(17P13.2) MUTATED     14    1
  DEL PEAK 13(17P13.2) WILD-TYPE   96   55
        clus
vv       DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE
  CLUS_1                            1                             55
  CLUS_2                           14                             96
D17V5, multiclass
        clus
vv       DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE
  CLUS_1                            4                             79
  CLUS_2                            7                             31
  CLUS_3                            4                             53
D17V6, multiclass
        clus
vv       DEL PEAK 13(17P13.2) MUTATED DEL PEAK 13(17P13.2) WILD-TYPE
  CLUS_1                            7                             30
  CLUS_2                            1                             78
  CLUS_3                            7                             55

Clustering(18) Variable = Del Peak 14(17q11.2) mutation analysis
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE
  CLUS_1                            9                             61
  CLUS_2                            2                             50
  CLUS_3                            2                             42
D18V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(17Q11.2) MUTATED     11    2
  DEL PEAK 14(17Q11.2) WILD-TYPE   99   54
        clus
vv       DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE
  CLUS_1                            2                             54
  CLUS_2                           11                             99
D18V5, multiclass
        clus
vv       DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE
  CLUS_1                            3                             80
  CLUS_2                            5                             33
  CLUS_3                            5                             52
D18V6, multiclass
        clus
vv       DEL PEAK 14(17Q11.2) MUTATED DEL PEAK 14(17Q11.2) WILD-TYPE
  CLUS_1                            5                             32
  CLUS_2                            1                             78
  CLUS_3                            7                             55

Clustering(19) Variable = Del Peak 15(18p11.21) mutation analysis
D19V1, multiclass
D19V2, multiclass
D19V3, multiclass
        clus
vv       DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE
  CLUS_1                             5                              65
  CLUS_2                             1                              51
  CLUS_3                             2                              42
D19V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(18P11.21) MUTATED      6    2
  DEL PEAK 15(18P11.21) WILD-TYPE  104   54
        clus
vv       DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE
  CLUS_1                             2                              54
  CLUS_2                             6                             104
D19V5, multiclass
        clus
vv       DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE
  CLUS_1                             3                              80
  CLUS_2                             4                              34
  CLUS_3                             1                              56
D19V6, multiclass
        clus
vv       DEL PEAK 15(18P11.21) MUTATED DEL PEAK 15(18P11.21) WILD-TYPE
  CLUS_1                             4                              33
  CLUS_2                             3                              76
  CLUS_3                             1                              61

Clustering(20) Variable = Del Peak 16(20q13.13) mutation analysis
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE
  CLUS_1                             2                              68
  CLUS_2                             1                              51
  CLUS_3                             0                              44
D20V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(20Q13.13) MUTATED      2    1
  DEL PEAK 16(20Q13.13) WILD-TYPE  108   55
        clus
vv       DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE
  CLUS_1                             1                              55
  CLUS_2                             2                             108
D20V5, multiclass
        clus
vv       DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE
  CLUS_1                             0                              83
  CLUS_2                             1                              37
  CLUS_3                             2                              55
D20V6, multiclass
        clus
vv       DEL PEAK 16(20Q13.13) MUTATED DEL PEAK 16(20Q13.13) WILD-TYPE
  CLUS_1                             1                              36
  CLUS_2                             0                              79
  CLUS_3                             2                              60
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
