
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_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/375890/broad_values_by_arm.mutsig.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 80 to 22."
[1]  22 191
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               188 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               188 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               187 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               187 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               187 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               187 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               20               171 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               20               171 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21               170 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21               170 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                188 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                188 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                187 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                187 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                184 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                184 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                188 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                188 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                188 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                188 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                186 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                186 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                186 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                186 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                183 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                183 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                183 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                183 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               185 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               185 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               176 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               15               176 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               18               173 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               18               173 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                188 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                188 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                181 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                181 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                186 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                186 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                186 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                186 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                188 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                188 
[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 = 1p gain mutation analysis
D1V1, multiclass
D1V2, multiclass
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                67
  CLUS_2               0                52
  CLUS_3               0                44
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE   56  107
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                56
  CLUS_2               3               107
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                82
  CLUS_2               2                36
  CLUS_3               0                57
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                35
  CLUS_2               0                79
  CLUS_3               1                61

Clustering(2) Variable = 4p gain mutation analysis
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2851        TCGA-AB-2853 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2856        TCGA-AB-2857        TCGA-AB-2858 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870        TCGA-AB-2871 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874        TCGA-AB-2875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917        TCGA-AB-2919 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    2
  4P GAIN WILD-TYPE   56  108
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                56
  CLUS_2               2               108
D2V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4                79
  CLUS_2               0                38
  CLUS_3               0                57
D2V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                37
  CLUS_2               2                77
  CLUS_3               2                60

Clustering(3) Variable = 4q gain mutation analysis
D3V1, multiclass
D3V2, multiclass
D3V3, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2820 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2821        TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2825        TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2832        TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2837        TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2841        TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2846        TCGA-AB-2848        TCGA-AB-2851        TCGA-AB-2853 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2856        TCGA-AB-2857        TCGA-AB-2858 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861        TCGA-AB-2862 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866        TCGA-AB-2867 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870        TCGA-AB-2871 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874        TCGA-AB-2875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880        TCGA-AB-2881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885        TCGA-AB-2886 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889        TCGA-AB-2890 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897        TCGA-AB-2898 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901        TCGA-AB-2903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909        TCGA-AB-2910 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913        TCGA-AB-2914 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917        TCGA-AB-2919 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924        TCGA-AB-2925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2929        TCGA-AB-2930 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    2
  4Q GAIN WILD-TYPE   56  108
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                56
  CLUS_2               2               108
D3V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4                79
  CLUS_2               0                38
  CLUS_3               0                57
D3V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                37
  CLUS_2               2                77
  CLUS_3               2                60

Clustering(4) Variable = 8p gain mutation analysis
D4V1, multiclass
D4V2, multiclass
D4V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              11                59
  CLUS_2               2                50
  CLUS_3               3                41
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   15
  8P GAIN WILD-TYPE   55   95
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                55
  CLUS_2              15                95
D4V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                75
  CLUS_2               8                30
  CLUS_3               3                54
D4V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                29
  CLUS_2               7                72
  CLUS_3               4                58

Clustering(5) Variable = 8q gain mutation analysis
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              12                58
  CLUS_2               2                50
  CLUS_3               3                41
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   16
  8Q GAIN WILD-TYPE   55   94
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                55
  CLUS_2              16                94
D5V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               8                75
  CLUS_2               8                30
  CLUS_3               4                53
D5V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               8                29
  CLUS_2               7                72
  CLUS_3               5                57

Clustering(6) Variable = 10q gain mutation analysis
D6V1, multiclass
D6V2, multiclass
D6V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                0                 52
  CLUS_3                0                 44
D6V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE   56  107
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                3                107
D6V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                1                 37
  CLUS_3                1                 56
D6V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 36
  CLUS_2                0                 79
  CLUS_3                2                 60

Clustering(7) Variable = 11p gain mutation analysis
D7V1, multiclass
D7V2, multiclass
D7V3, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                1                 51
  CLUS_3                0                 44
D7V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    3
  11P GAIN WILD-TYPE   55  107
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
D7V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                2                 36
  CLUS_3                1                 56
D7V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 35
  CLUS_2                0                 79
  CLUS_3                2                 60

Clustering(8) Variable = 11q gain mutation analysis
D8V1, multiclass
D8V2, multiclass
D8V3, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                 64
  CLUS_2                1                 51
  CLUS_3                0                 44
D8V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    6
  11Q GAIN WILD-TYPE   55  104
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                6                104
D8V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 80
  CLUS_2                3                 35
  CLUS_3                1                 56
D8V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 34
  CLUS_2                2                 77
  CLUS_3                2                 60

Clustering(9) Variable = 13q gain mutation analysis
D9V1, multiclass
D9V2, multiclass
D9V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                0                 52
  CLUS_3                0                 44
D9V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    3
  13Q GAIN WILD-TYPE   56  107
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                3                107
D9V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                1                 37
  CLUS_3                0                 57
D9V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 36
  CLUS_2                0                 79
  CLUS_3                2                 60

Clustering(10) Variable = 17q gain mutation analysis
D10V1, multiclass
D10V2, multiclass
D10V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 69
  CLUS_2                1                 51
  CLUS_3                1                 43
D10V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    3
  17Q GAIN WILD-TYPE   56  107
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                3                107
D10V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                1                 37
  CLUS_3                0                 57
D10V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 36
  CLUS_2                0                 79
  CLUS_3                2                 60

Clustering(11) Variable = 19p gain mutation analysis
D11V1, multiclass
D11V2, multiclass
D11V3, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 51
  CLUS_3                1                 43
D11V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE   55  107
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
D11V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                 79
  CLUS_2                0                 38
  CLUS_3                1                 56
D11V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 37
  CLUS_2                2                 77
  CLUS_3                3                 59

Clustering(12) Variable = 19q gain mutation analysis
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 51
  CLUS_3                1                 43
D12V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    3
  19Q GAIN WILD-TYPE   55  107
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
D12V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 79
  CLUS_2                0                 38
  CLUS_3                1                 56
D12V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 37
  CLUS_2                2                 77
  CLUS_3                3                 59

Clustering(13) Variable = 21q gain mutation analysis
D13V1, multiclass
D13V2, multiclass
D13V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 65
  CLUS_2                1                 51
  CLUS_3                0                 44
D13V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    4
  21Q GAIN WILD-TYPE   54  106
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 54
  CLUS_2                4                106
D13V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                2                 36
  CLUS_3                4                 53
D13V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 35
  CLUS_2                1                 78
  CLUS_3                4                 58

Clustering(14) Variable = 22q gain mutation analysis
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                 63
  CLUS_2                1                 51
  CLUS_3                0                 44
D14V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    7
  22Q GAIN WILD-TYPE   55  103
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                7                103
D14V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                4                 34
  CLUS_3                2                 55
D14V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 33
  CLUS_2                1                 78
  CLUS_3                3                 59

Clustering(15) Variable = 5q loss mutation analysis
D15V1, multiclass
D15V2, multiclass
D15V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                66
  CLUS_2               1                51
  CLUS_3               0                44
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    4
  5Q LOSS WILD-TYPE   55  106
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                55
  CLUS_2               4               106
D15V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                83
  CLUS_2               3                35
  CLUS_3               2                55
D15V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                34
  CLUS_2               0                79
  CLUS_3               2                60

Clustering(16) Variable = 7p loss mutation analysis
D16V1, multiclass
D16V2, multiclass
D16V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              11                59
  CLUS_2               0                52
  CLUS_3               3                41
D16V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   14
  7P LOSS WILD-TYPE   56   96
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                56
  CLUS_2              14                96
D16V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               8                30
  CLUS_3               4                53
D16V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               8                29
  CLUS_2               3                76
  CLUS_3               4                58

Clustering(17) Variable = 7q loss mutation analysis
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              11                59
  CLUS_2               1                51
  CLUS_3               3                41
D17V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   14
  7Q LOSS WILD-TYPE   55   96
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                55
  CLUS_2              14                96
D17V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               3                80
  CLUS_2               9                29
  CLUS_3               5                52
D17V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               9                28
  CLUS_2               3                76
  CLUS_3               5                57

Clustering(18) Variable = 12p loss mutation analysis
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                0                 52
  CLUS_3                1                 43
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    3
  12P LOSS WILD-TYPE   56  107
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                3                107
D18V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                1                 37
  CLUS_3                1                 56
D18V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 36
  CLUS_2                0                 79
  CLUS_3                2                 60

Clustering(19) Variable = 17p loss mutation analysis
D19V1, multiclass
D19V2, multiclass
D19V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                8                 62
  CLUS_2                1                 51
  CLUS_3                1                 43
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    9
  17P LOSS WILD-TYPE   55  101
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                9                101
D19V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 81
  CLUS_2                6                 32
  CLUS_3                2                 55
D19V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                 31
  CLUS_2                1                 78
  CLUS_3                3                 59

Clustering(20) Variable = 17q loss mutation analysis
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 66
  CLUS_2                1                 51
  CLUS_3                0                 44
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    4
  17Q LOSS WILD-TYPE   55  106
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                4                106
D20V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                4                 34
  CLUS_3                1                 56
D20V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 33
  CLUS_2                0                 79
  CLUS_3                1                 61

Clustering(21) Variable = 18p loss mutation analysis
D21V1, multiclass
D21V2, multiclass
D21V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 51
  CLUS_3                1                 43
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    3
  18P LOSS WILD-TYPE   55  107
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
D21V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 82
  CLUS_2                2                 36
  CLUS_3                1                 56
D21V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 35
  CLUS_2                1                 78
  CLUS_3                1                 61

Clustering(22) Variable = 18q loss mutation analysis
D22V1, multiclass
D22V2, multiclass
D22V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 51
  CLUS_3                0                 44
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    2
  18Q LOSS WILD-TYPE   55  108
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                2                108
D22V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 83
  CLUS_2                2                 36
  CLUS_3                1                 56
D22V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 35
  CLUS_2                0                 79
  CLUS_3                1                 61
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
