
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/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/Correlate_Genomic_Events.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/GDAC_Correlate_Genomic_Events/broadinstitute.org/cancer.genome.analysis/10441/13/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-tTRUE", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/6159621/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/6159589/LAML-TB.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LAML-TB", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "terrence_modification_tag"
[1] TRUE
[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" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/6159589/LAML-TB.transferedmergedcluster.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/6159621/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=191, common to both=191
[1] "Reduce the number of clustering variables from 80 to 30."
[1]  30 191
[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 
               22               169 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22               169 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               168 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               168 
[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 
                 6                185 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                185 
[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 
                 9                182 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                182 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               188 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               188 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               188 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               188 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               188 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               188 
[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 
               17               174 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               174 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               20               171 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               20               171 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                187 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                187 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                187 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                187 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                187 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                187 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                178 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                178 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                184 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                184 
[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 
                 4                187 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                187 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                187 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                187 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                187 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                187 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               186 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               186 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection="
[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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=5,	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=4,	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=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        0      2      1      0
  1P GAIN WILD-TYPE    147     12     26      3
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0               147
  CLUS_2               2                12
  CLUS_3               1                26
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  1P GAIN MUTATED        0      0      3      0      0
  1P GAIN WILD-TYPE     46     44     58     14     20
D1V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        3      0      0
  1P GAIN WILD-TYPE     67     52     44
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
                   cls
clus                  0   1
  1P GAIN MUTATED     0   3
  1P GAIN WILD-TYPE  56 107
[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
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  1P GAIN MUTATED        0      2      0      1
  1P GAIN WILD-TYPE     58     35     41     42
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                58
  CLUS_2               2                35
  CLUS_3               0                41
  CLUS_4               1                42
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  1P GAIN MUTATED        2      0      1
  1P GAIN WILD-TYPE     33     79     64
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                33
  CLUS_2               0                79
  CLUS_3               1                64

Clustering(2) Variable = 4P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        1      0      3      0
  4P GAIN WILD-TYPE    146     14     24      3
D2V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1               146
  CLUS_2               0                14
  CLUS_3               3                24
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4P GAIN MUTATED        2      0      0      0      2
  4P GAIN WILD-TYPE     44     44     61     14     18
D2V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        1      0      1
  4P GAIN WILD-TYPE     69     52     43
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
                   cls
clus                  0   1
  4P GAIN MUTATED     0   2
  4P GAIN WILD-TYPE  56 108
[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
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4P GAIN MUTATED        3      0      0      1
  4P GAIN WILD-TYPE     55     37     41     42
D2V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                55
  CLUS_2               0                37
  CLUS_3               0                41
  CLUS_4               1                42
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4P GAIN MUTATED        0      2      2
  4P GAIN WILD-TYPE     35     77     63
D2V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                35
  CLUS_2               2                77
  CLUS_3               2                63

Clustering(3) Variable = 4Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        1      0      3      0
  4Q GAIN WILD-TYPE    146     14     24      3
D3V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1               146
  CLUS_2               0                14
  CLUS_3               3                24
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  4Q GAIN MUTATED        2      0      0      0      2
  4Q GAIN WILD-TYPE     44     44     61     14     18
D3V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        1      0      1
  4Q GAIN WILD-TYPE     69     52     43
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
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   2
  4Q GAIN WILD-TYPE  56 108
[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
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  4Q GAIN MUTATED        3      0      0      1
  4Q GAIN WILD-TYPE     55     37     41     42
D3V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                55
  CLUS_2               0                37
  CLUS_3               0                41
  CLUS_4               1                42
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  4Q GAIN MUTATED        0      2      2
  4Q GAIN WILD-TYPE     35     77     63
D3V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                35
  CLUS_2               2                77
  CLUS_3               2                63

Clustering(4) Variable = 8P GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED       11      1     10      0
  8P GAIN WILD-TYPE    136     13     17      3
D4V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              11               136
  CLUS_2               1                13
  CLUS_3              10                17
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8P GAIN MUTATED        2      1     16      0      2
  8P GAIN WILD-TYPE     44     43     45     14     18
D4V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED       13      2      3
  8P GAIN WILD-TYPE     57     50     41
D4V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              13                57
  CLUS_2               2                50
  CLUS_3               3                41
D4V4, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    1 17
  8P GAIN WILD-TYPE 55 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   17
  8P GAIN WILD-TYPE   55   93
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                55
  CLUS_2              17                93
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8P GAIN MUTATED        2      9      3      7
  8P GAIN WILD-TYPE     56     28     38     36
D4V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                56
  CLUS_2               9                28
  CLUS_3               3                38
  CLUS_4               7                36
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8P GAIN MUTATED        8      7      6
  8P GAIN WILD-TYPE     27     72     59
D4V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                27
  CLUS_2               7                72
  CLUS_3               6                59

Clustering(5) Variable = 8Q GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED       12      1     10      0
  8Q GAIN WILD-TYPE    135     13     17      3
D5V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              12               135
  CLUS_2               1                13
  CLUS_3              10                17
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  8Q GAIN MUTATED        2      2     16      0      2
  8Q GAIN WILD-TYPE     44     42     45     14     18
D5V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED       14      2      3
  8Q GAIN WILD-TYPE     56     50     41
D5V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                56
  CLUS_2               2                50
  CLUS_3               3                41
D5V4, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1 18
  8Q GAIN WILD-TYPE 55 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   18
  8Q GAIN WILD-TYPE   55   92
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                55
  CLUS_2              18                92
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  8Q GAIN MUTATED        2      9      3      8
  8Q GAIN WILD-TYPE     56     28     38     35
D5V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                56
  CLUS_2               9                28
  CLUS_3               3                38
  CLUS_4               8                35
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  8Q GAIN MUTATED        8      7      7
  8Q GAIN WILD-TYPE     27     72     58
D5V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               8                27
  CLUS_2               7                72
  CLUS_3               7                58

Clustering(6) Variable = 10Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        0      1      2      0
  10Q GAIN WILD-TYPE    147     13     25      3
D6V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                1                 13
  CLUS_3                2                 25
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  10Q GAIN MUTATED        0      0      3      0      0
  10Q GAIN WILD-TYPE     46     44     58     14     20
D6V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        3      0      0
  10Q GAIN WILD-TYPE     67     52     44
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
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   3
  10Q GAIN WILD-TYPE  56 107
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  10Q GAIN MUTATED        0      1      1      1
  10Q GAIN WILD-TYPE     58     36     40     42
D6V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                1                 36
  CLUS_3                1                 40
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  10Q GAIN MUTATED        1      0      2
  10Q GAIN WILD-TYPE     34     79     63
D6V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                0                 79
  CLUS_3                2                 63

Clustering(7) Variable = 11P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        0      3      1      0
  11P GAIN WILD-TYPE    147     11     26      3
D7V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                3                 11
  CLUS_3                1                 26
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11P GAIN MUTATED        0      0      4      0      0
  11P GAIN WILD-TYPE     46     44     57     14     20
D7V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        3      1      0
  11P GAIN WILD-TYPE     67     51     44
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
                    cls
clus                   0   1
  11P GAIN MUTATED     1   3
  11P GAIN WILD-TYPE  55 107
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11P GAIN MUTATED        1      2      0      1
  11P GAIN WILD-TYPE     57     35     41     42
D7V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 57
  CLUS_2                2                 35
  CLUS_3                0                 41
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11P GAIN MUTATED        2      0      2
  11P GAIN WILD-TYPE     33     79     63
D7V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                0                 79
  CLUS_3                2                 63

Clustering(8) Variable = 11Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        0      4      3      0
  11Q GAIN WILD-TYPE    147     10     24      3
D8V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                4                 10
  CLUS_3                3                 24
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  11Q GAIN MUTATED        0      0      7      0      0
  11Q GAIN WILD-TYPE     46     44     54     14     20
D8V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        6      1      0
  11Q GAIN WILD-TYPE     64     51     44
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
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   6
  11Q GAIN WILD-TYPE  55 104
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  11Q GAIN MUTATED        2      3      0      2
  11Q GAIN WILD-TYPE     56     34     41     41
D8V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 56
  CLUS_2                3                 34
  CLUS_3                0                 41
  CLUS_4                2                 41
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  11Q GAIN MUTATED        3      2      2
  11Q GAIN WILD-TYPE     32     77     63
D8V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 32
  CLUS_2                2                 77
  CLUS_3                2                 63

Clustering(9) Variable = 13Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        2      1      3      0
  13Q GAIN WILD-TYPE    145     13     24      3
D9V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                145
  CLUS_2                1                 13
  CLUS_3                3                 24
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  13Q GAIN MUTATED        0      0      6      0      0
  13Q GAIN WILD-TYPE     46     44     55     14     20
D9V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        5      1      0
  13Q GAIN WILD-TYPE     65     51     44
D9V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                 65
  CLUS_2                1                 51
  CLUS_3                0                 44
D9V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   6
  13Q GAIN WILD-TYPE  56 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    6
  13Q GAIN WILD-TYPE   56  104
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                6                104
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  13Q GAIN MUTATED        1      1      2      2
  13Q GAIN WILD-TYPE     57     36     39     41
D9V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 57
  CLUS_2                1                 36
  CLUS_3                2                 39
  CLUS_4                2                 41
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  13Q GAIN MUTATED        1      1      4
  13Q GAIN WILD-TYPE     34     78     61
D9V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                1                 78
  CLUS_3                4                 61

Clustering(10) Variable = 17Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        0      0      3      0
  17Q GAIN WILD-TYPE    147     14     24      3
D10V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                3                 24
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q GAIN MUTATED        0      0      2      0      1
  17Q GAIN WILD-TYPE     46     44     59     14     19
D10V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        1      1      1
  17Q GAIN WILD-TYPE     69     51     43
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
                    cls
clus                   0   1
  17Q GAIN MUTATED     0   3
  17Q GAIN WILD-TYPE  56 107
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q GAIN MUTATED        2      1      0      0
  17Q GAIN WILD-TYPE     56     36     41     43
D10V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 56
  CLUS_2                1                 36
  CLUS_3                0                 41
  CLUS_4                0                 43
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q GAIN MUTATED        1      0      2
  17Q GAIN WILD-TYPE     34     79     63
D10V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                0                 79
  CLUS_3                2                 63

Clustering(11) Variable = 19P GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        0      1      4      0
  19P GAIN WILD-TYPE    147     13     23      3
D11V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                1                 13
  CLUS_3                4                 23
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P GAIN MUTATED        2      0      2      0      1
  19P GAIN WILD-TYPE     44     44     59     14     19
D11V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        2      1      1
  19P GAIN WILD-TYPE     68     51     43
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
                    cls
clus                   0   1
  19P GAIN MUTATED     1   3
  19P GAIN WILD-TYPE  55 107
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P GAIN MUTATED        3      1      0      1
  19P GAIN WILD-TYPE     55     36     41     42
D11V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 55
  CLUS_2                1                 36
  CLUS_3                0                 41
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P GAIN MUTATED        1      2      2
  19P GAIN WILD-TYPE     34     77     63
D11V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                2                 77
  CLUS_3                2                 63

Clustering(12) Variable = 19Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        0      1      4      0
  19Q GAIN WILD-TYPE    147     13     23      3
D12V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                1                 13
  CLUS_3                4                 23
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q GAIN MUTATED        2      0      2      0      1
  19Q GAIN WILD-TYPE     44     44     59     14     19
D12V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        2      1      1
  19Q GAIN WILD-TYPE     68     51     43
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
                    cls
clus                   0   1
  19Q GAIN MUTATED     1   3
  19Q GAIN WILD-TYPE  55 107
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q GAIN MUTATED        3      1      0      1
  19Q GAIN WILD-TYPE     55     36     41     42
D12V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                 55
  CLUS_2                1                 36
  CLUS_3                0                 41
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q GAIN MUTATED        1      2      2
  19Q GAIN WILD-TYPE     34     77     63
D12V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                2                 77
  CLUS_3                2                 63

Clustering(13) Variable = 21Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        0      0      8      0
  21Q GAIN WILD-TYPE    147     14     19      3
D13V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                8                 19
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  21Q GAIN MUTATED        1      0      5      0      1
  21Q GAIN WILD-TYPE     45     44     56     14     19
D13V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        5      1      0
  21Q GAIN WILD-TYPE     65     51     44
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
                    cls
clus                   0   1
  21Q GAIN MUTATED     2   4
  21Q GAIN WILD-TYPE  54 106
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  21Q GAIN MUTATED        1      2      4      0
  21Q GAIN WILD-TYPE     57     35     37     43
D13V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 57
  CLUS_2                2                 35
  CLUS_3                4                 37
  CLUS_4                0                 43
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  21Q GAIN MUTATED        2      1      4
  21Q GAIN WILD-TYPE     33     78     61
D13V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                1                 78
  CLUS_3                4                 61

Clustering(14) Variable = 22Q GAIN MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        2      2      5      0
  22Q GAIN WILD-TYPE    145     12     22      3
D14V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                145
  CLUS_2                2                 12
  CLUS_3                5                 22
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  22Q GAIN MUTATED        0      1      8      0      0
  22Q GAIN WILD-TYPE     46     43     53     14     20
D14V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        7      1      1
  22Q GAIN WILD-TYPE     63     51     43
D14V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                 63
  CLUS_2                1                 51
  CLUS_3                1                 43
D14V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1   8
  22Q GAIN WILD-TYPE  55 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    8
  22Q GAIN WILD-TYPE   55  102
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                8                102
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  22Q GAIN MUTATED        0      4      2      3
  22Q GAIN WILD-TYPE     58     33     39     40
D14V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                4                 33
  CLUS_3                2                 39
  CLUS_4                3                 40
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  22Q GAIN MUTATED        4      2      3
  22Q GAIN WILD-TYPE     31     77     62
D14V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 31
  CLUS_2                2                 77
  CLUS_3                3                 62

Clustering(15) Variable = XQ GAIN MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        0      1      1      1
  XQ GAIN WILD-TYPE    147     13     26      2
D15V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0               147
  CLUS_2               1                13
  CLUS_3               1                26
  CLUS_4               1                 2
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ GAIN MUTATED        1      0      2      0      0
  XQ GAIN WILD-TYPE     45     44     59     14     20
D15V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        2      0      0
  XQ GAIN WILD-TYPE     68     52     44
D15V3, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               164 
       TCGA-AB-2803        TCGA-AB-2805        TCGA-AB-2806        TCGA-AB-2807 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2808        TCGA-AB-2810        TCGA-AB-2811        TCGA-AB-2812 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2813        TCGA-AB-2814        TCGA-AB-2815        TCGA-AB-2816 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2817        TCGA-AB-2818        TCGA-AB-2819        TCGA-AB-2821 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2822        TCGA-AB-2823        TCGA-AB-2824        TCGA-AB-2825 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2826        TCGA-AB-2828        TCGA-AB-2830        TCGA-AB-2832 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2834        TCGA-AB-2835        TCGA-AB-2836        TCGA-AB-2837 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2838        TCGA-AB-2839        TCGA-AB-2840        TCGA-AB-2841 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2842        TCGA-AB-2844        TCGA-AB-2845        TCGA-AB-2846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2848        TCGA-AB-2849        TCGA-AB-2851        TCGA-AB-2853 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2854        TCGA-AB-2855        TCGA-AB-2856        TCGA-AB-2857 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2858        TCGA-AB-2859        TCGA-AB-2860        TCGA-AB-2861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2862        TCGA-AB-2863        TCGA-AB-2865        TCGA-AB-2866 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2867        TCGA-AB-2868        TCGA-AB-2869        TCGA-AB-2870 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2871        TCGA-AB-2872        TCGA-AB-2873        TCGA-AB-2874 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2875        TCGA-AB-2877        TCGA-AB-2879        TCGA-AB-2880 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2881        TCGA-AB-2882        TCGA-AB-2884        TCGA-AB-2885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2886        TCGA-AB-2887        TCGA-AB-2888        TCGA-AB-2889 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2890        TCGA-AB-2895        TCGA-AB-2896        TCGA-AB-2897 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2898        TCGA-AB-2899        TCGA-AB-2900        TCGA-AB-2901 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2903        TCGA-AB-2904        TCGA-AB-2908        TCGA-AB-2909 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2910        TCGA-AB-2911        TCGA-AB-2912        TCGA-AB-2913 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2914        TCGA-AB-2915        TCGA-AB-2916        TCGA-AB-2917 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2919        TCGA-AB-2920        TCGA-AB-2921        TCGA-AB-2924 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2925        TCGA-AB-2927        TCGA-AB-2928        TCGA-AB-2930 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2931        TCGA-AB-2932        TCGA-AB-2933        TCGA-AB-2934 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2935        TCGA-AB-2936        TCGA-AB-2937        TCGA-AB-2938 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2939        TCGA-AB-2940        TCGA-AB-2941        TCGA-AB-2942 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2943        TCGA-AB-2944        TCGA-AB-2946        TCGA-AB-2948 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2949        TCGA-AB-2950        TCGA-AB-2952        TCGA-AB-2954 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2955        TCGA-AB-2956        TCGA-AB-2959        TCGA-AB-2963 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2964        TCGA-AB-2965        TCGA-AB-2966        TCGA-AB-2967 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2969        TCGA-AB-2970        TCGA-AB-2971        TCGA-AB-2972 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2973        TCGA-AB-2975        TCGA-AB-2976        TCGA-AB-2977 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2978        TCGA-AB-2980        TCGA-AB-2982        TCGA-AB-2983 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2984        TCGA-AB-2985        TCGA-AB-2986        TCGA-AB-2987 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2988        TCGA-AB-2990        TCGA-AB-2991        TCGA-AB-2992 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2993        TCGA-AB-2994        TCGA-AB-2995        TCGA-AB-2996 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-2998        TCGA-AB-2999        TCGA-AB-3000        TCGA-AB-3001 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-3002        TCGA-AB-3005        TCGA-AB-3006        TCGA-AB-3007 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AB-3008        TCGA-AB-3009        TCGA-AB-3011        TCGA-AB-3012 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D15V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   2
  XQ GAIN WILD-TYPE  56 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    2
  XQ GAIN WILD-TYPE   56  108
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                56
  CLUS_2               2               108
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ GAIN MUTATED        1      1      0      1
  XQ GAIN WILD-TYPE     57     36     41     42
D15V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                57
  CLUS_2               1                36
  CLUS_3               0                41
  CLUS_4               1                42
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ GAIN MUTATED        1      1      1
  XQ GAIN WILD-TYPE     34     78     64
D15V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                34
  CLUS_2               1                78
  CLUS_3               1                64

Clustering(16) Variable = 3P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      0      3      0
  3P LOSS WILD-TYPE    147     14     24      3
D16V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0               147
  CLUS_2               0                14
  CLUS_3               3                24
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3P LOSS MUTATED        0      0      3      0      0
  3P LOSS WILD-TYPE     46     44     58     14     20
D16V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        2      1      0
  3P LOSS WILD-TYPE     68     51     44
D16V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                68
  CLUS_2               1                51
  CLUS_3               0                44
D16V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1   2
  3P LOSS WILD-TYPE  55 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    2
  3P LOSS WILD-TYPE   55  108
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                55
  CLUS_2               2               108
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3P LOSS MUTATED        0      2      1      0
  3P LOSS WILD-TYPE     58     35     40     43
D16V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                58
  CLUS_2               2                35
  CLUS_3               1                40
  CLUS_4               0                43
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3P LOSS MUTATED        2      0      1
  3P LOSS WILD-TYPE     33     79     64
D16V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                33
  CLUS_2               0                79
  CLUS_3               1                64

Clustering(17) Variable = 3Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        0      0      3      0
  3Q LOSS WILD-TYPE    147     14     24      3
D17V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0               147
  CLUS_2               0                14
  CLUS_3               3                24
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  3Q LOSS MUTATED        0      0      3      0      0
  3Q LOSS WILD-TYPE     46     44     58     14     20
D17V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        2      1      0
  3Q LOSS WILD-TYPE     68     51     44
D17V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                68
  CLUS_2               1                51
  CLUS_3               0                44
D17V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1   2
  3Q LOSS WILD-TYPE  55 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    2
  3Q LOSS WILD-TYPE   55  108
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                55
  CLUS_2               2               108
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  3Q LOSS MUTATED        0      2      1      0
  3Q LOSS WILD-TYPE     58     35     40     43
D17V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                58
  CLUS_2               2                35
  CLUS_3               1                40
  CLUS_4               0                43
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  3Q LOSS MUTATED        2      0      1
  3Q LOSS WILD-TYPE     33     79     64
D17V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                33
  CLUS_2               0                79
  CLUS_3               1                64

Clustering(18) Variable = 5Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        0      0      6      0
  5Q LOSS WILD-TYPE    147     14     21      3
D18V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0               147
  CLUS_2               0                14
  CLUS_3               6                21
  CLUS_4               0                 3
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  5Q LOSS MUTATED        0      0      6      0      0
  5Q LOSS WILD-TYPE     46     44     55     14     20
D18V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        4      1      0
  5Q LOSS WILD-TYPE     66     51     44
D18V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                66
  CLUS_2               1                51
  CLUS_3               0                44
D18V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1   4
  5Q LOSS WILD-TYPE  55 106
[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
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  5Q LOSS MUTATED        0      3      2      0
  5Q LOSS WILD-TYPE     58     34     39     43
D18V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                58
  CLUS_2               3                34
  CLUS_3               2                39
  CLUS_4               0                43
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  5Q LOSS MUTATED        3      0      2
  5Q LOSS WILD-TYPE     32     79     63
D18V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                32
  CLUS_2               0                79
  CLUS_3               2                63

Clustering(19) Variable = 7P LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        7      0      8      2
  7P LOSS WILD-TYPE    140     14     19      1
D19V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               7               140
  CLUS_2               0                14
  CLUS_3               8                19
  CLUS_4               2                 1
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7P LOSS MUTATED        1      0     14      1      1
  7P LOSS WILD-TYPE     45     44     47     13     19
D19V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       13      0      3
  7P LOSS WILD-TYPE     57     52     41
D19V3, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              13                57
  CLUS_2               0                52
  CLUS_3               3                41
D19V4, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0 16
  7P LOSS WILD-TYPE 56 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   16
  7P LOSS WILD-TYPE   56   94
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                56
  CLUS_2              16                94
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7P LOSS MUTATED        1      9      3      4
  7P LOSS WILD-TYPE     57     28     38     39
D19V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                57
  CLUS_2               9                28
  CLUS_3               3                38
  CLUS_4               4                39
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7P LOSS MUTATED       10      2      5
  7P LOSS WILD-TYPE     25     77     60
D19V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1              10                25
  CLUS_2               2                77
  CLUS_3               5                60

Clustering(20) Variable = 7Q LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        8      0     10      2
  7Q LOSS WILD-TYPE    139     14     17      1
D20V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               8               139
  CLUS_2               0                14
  CLUS_3              10                17
  CLUS_4               2                 1
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  7Q LOSS MUTATED        1      0     17      1      1
  7Q LOSS WILD-TYPE     45     44     44     13     19
D20V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       13      1      3
  7Q LOSS WILD-TYPE     57     51     41
D20V3, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              13                57
  CLUS_2               1                51
  CLUS_3               3                41
D20V4, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    1 16
  7Q LOSS WILD-TYPE 55 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   16
  7Q LOSS WILD-TYPE   55   94
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                55
  CLUS_2              16                94
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  7Q LOSS MUTATED        1     10      4      4
  7Q LOSS WILD-TYPE     57     27     37     39
D20V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                57
  CLUS_2              10                27
  CLUS_3               4                37
  CLUS_4               4                39
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  7Q LOSS MUTATED       11      2      6
  7Q LOSS WILD-TYPE     24     77     59
D20V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1              11                24
  CLUS_2               2                77
  CLUS_3               6                59

Clustering(21) Variable = 12P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        1      0      2      1
  12P LOSS WILD-TYPE    146     14     25      2
D21V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                146
  CLUS_2                0                 14
  CLUS_3                2                 25
  CLUS_4                1                  2
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  12P LOSS MUTATED        0      0      2      0      2
  12P LOSS WILD-TYPE     46     44     59     14     18
D21V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED        3      0      1
  12P LOSS WILD-TYPE     67     52     43
D21V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                0                 52
  CLUS_3                1                 43
D21V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0   4
  12P LOSS WILD-TYPE  56 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    4
  12P LOSS WILD-TYPE   56  106
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                4                106
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  12P LOSS MUTATED        1      2      1      0
  12P LOSS WILD-TYPE     57     35     40     43
D21V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 57
  CLUS_2                2                 35
  CLUS_3                1                 40
  CLUS_4                0                 43
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  12P LOSS MUTATED        2      0      2
  12P LOSS WILD-TYPE     33     79     63
D21V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                0                 79
  CLUS_3                2                 63

Clustering(22) Variable = 15Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      0      3      1
  15Q LOSS WILD-TYPE    147     14     24      2
D22V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                3                 24
  CLUS_4                1                  2
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  15Q LOSS MUTATED        0      1      2      0      1
  15Q LOSS WILD-TYPE     46     43     59     14     19
D22V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        4      0      0
  15Q LOSS WILD-TYPE     66     52     44
D22V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 66
  CLUS_2                0                 52
  CLUS_3                0                 44
D22V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0   4
  15Q LOSS WILD-TYPE  56 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0    4
  15Q LOSS WILD-TYPE   56  106
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 56
  CLUS_2                4                106
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  15Q LOSS MUTATED        0      3      0      1
  15Q LOSS WILD-TYPE     58     34     41     42
D22V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                3                 34
  CLUS_3                0                 41
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  15Q LOSS MUTATED        3      0      1
  15Q LOSS WILD-TYPE     32     79     64
D22V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 32
  CLUS_2                0                 79
  CLUS_3                1                 64

Clustering(23) Variable = 16Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      0      4      0
  16Q LOSS WILD-TYPE    147     14     23      3
D23V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                4                 23
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  16Q LOSS MUTATED        0      0      4      0      0
  16Q LOSS WILD-TYPE     46     44     57     14     20
D23V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        2      1      0
  16Q LOSS WILD-TYPE     68     51     44
D23V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 51
  CLUS_3                0                 44
D23V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1   2
  16Q LOSS WILD-TYPE  55 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE   55  108
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                2                108
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  16Q LOSS MUTATED        0      3      1      0
  16Q LOSS WILD-TYPE     58     34     40     43
D23V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                3                 34
  CLUS_3                1                 40
  CLUS_4                0                 43
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  16Q LOSS MUTATED        3      0      1
  16Q LOSS WILD-TYPE     32     79     64
D23V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 32
  CLUS_2                0                 79
  CLUS_3                1                 64

Clustering(24) Variable = 17P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        0      0     13      0
  17P LOSS WILD-TYPE    147     14     14      3
D24V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3               13                 14
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17P LOSS MUTATED        0      1     10      0      2
  17P LOSS WILD-TYPE     46     43     51     14     18
D24V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        9      2      2
  17P LOSS WILD-TYPE     61     50     42
D24V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                9                 61
  CLUS_2                2                 50
  CLUS_3                2                 42
D24V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1 12
  17P LOSS WILD-TYPE 55 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   12
  17P LOSS WILD-TYPE   55   98
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2               12                 98
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17P LOSS MUTATED        2      6      2      3
  17P LOSS WILD-TYPE     56     31     39     40
D24V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 56
  CLUS_2                6                 31
  CLUS_3                2                 39
  CLUS_4                3                 40
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17P LOSS MUTATED        6      1      6
  17P LOSS WILD-TYPE     29     78     59
D24V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                 29
  CLUS_2                1                 78
  CLUS_3                6                 59

Clustering(25) Variable = 17Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        0      0      7      0
  17Q LOSS WILD-TYPE    147     14     20      3
D25V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                7                 20
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  17Q LOSS MUTATED        0      1      5      0      1
  17Q LOSS WILD-TYPE     46     43     56     14     19
D25V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        6      1      0
  17Q LOSS WILD-TYPE     64     51     44
D25V3, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                6                 64
  CLUS_2                1                 51
  CLUS_3                0                 44
D25V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1   6
  17Q LOSS WILD-TYPE  55 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    6
  17Q LOSS WILD-TYPE   55  104
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                6                104
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  17Q LOSS MUTATED        0      4      1      2
  17Q LOSS WILD-TYPE     58     33     40     41
D25V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                4                 33
  CLUS_3                1                 40
  CLUS_4                2                 41
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  17Q LOSS MUTATED        4      0      3
  17Q LOSS WILD-TYPE     31     79     62
D25V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 31
  CLUS_2                0                 79
  CLUS_3                3                 62

Clustering(26) Variable = 18P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        0      0      5      0
  18P LOSS WILD-TYPE    147     14     22      3
D26V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                5                 22
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18P LOSS MUTATED        0      0      5      0      0
  18P LOSS WILD-TYPE     46     44     56     14     20
D26V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        2      1      1
  18P LOSS WILD-TYPE     68     51     43
D26V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 51
  CLUS_3                1                 43
D26V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1   3
  18P LOSS WILD-TYPE  55 107
[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
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18P LOSS MUTATED        0      2      1      1
  18P LOSS WILD-TYPE     58     35     40     42
D26V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                2                 35
  CLUS_3                1                 40
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18P LOSS MUTATED        2      1      1
  18P LOSS WILD-TYPE     33     78     64
D26V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                1                 78
  CLUS_3                1                 64

Clustering(27) Variable = 18Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        0      0      4      0
  18Q LOSS WILD-TYPE    147     14     23      3
D27V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                0                 14
  CLUS_3                4                 23
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  18Q LOSS MUTATED        0      0      4      0      0
  18Q LOSS WILD-TYPE     46     44     57     14     20
D27V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        3      1      0
  18Q LOSS WILD-TYPE     67     51     44
D27V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                1                 51
  CLUS_3                0                 44
D27V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1   3
  18Q LOSS WILD-TYPE  55 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE   55  107
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  18Q LOSS MUTATED        0      2      2      0
  18Q LOSS WILD-TYPE     58     35     39     43
D27V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                2                 35
  CLUS_3                2                 39
  CLUS_4                0                 43
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  18Q LOSS MUTATED        2      0      2
  18Q LOSS WILD-TYPE     33     79     63
D27V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                0                 79
  CLUS_3                2                 63

Clustering(28) Variable = 19P LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        0      1      3      0
  19P LOSS WILD-TYPE    147     13     24      3
D28V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                1                 13
  CLUS_3                3                 24
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19P LOSS MUTATED        0      1      3      0      0
  19P LOSS WILD-TYPE     46     43     58     14     20
D28V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        3      1      0
  19P LOSS WILD-TYPE     67     51     44
D28V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                1                 51
  CLUS_3                0                 44
D28V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1   3
  19P LOSS WILD-TYPE  55 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    3
  19P LOSS WILD-TYPE   55  107
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19P LOSS MUTATED        0      1      2      1
  19P LOSS WILD-TYPE     58     36     39     42
D28V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                1                 36
  CLUS_3                2                 39
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19P LOSS MUTATED        1      0      3
  19P LOSS WILD-TYPE     34     79     62
D28V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                0                 79
  CLUS_3                3                 62

Clustering(29) Variable = 19Q LOSS MUTATION ANALYSIS
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        0      1      3      0
  19Q LOSS WILD-TYPE    147     13     24      3
D29V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                147
  CLUS_2                1                 13
  CLUS_3                3                 24
  CLUS_4                0                  3
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  19Q LOSS MUTATED        0      1      3      0      0
  19Q LOSS WILD-TYPE     46     43     58     14     20
D29V2, multiclass
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED        3      1      0
  19Q LOSS WILD-TYPE     67     51     44
D29V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 67
  CLUS_2                1                 51
  CLUS_3                0                 44
D29V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   3
  19Q LOSS WILD-TYPE  55 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    3
  19Q LOSS WILD-TYPE   55  107
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 55
  CLUS_2                3                107
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3 CLUS_4
  19Q LOSS MUTATED        0      1      2      1
  19Q LOSS WILD-TYPE     58     36     39     42
D29V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 58
  CLUS_2                1                 36
  CLUS_3                2                 39
  CLUS_4                1                 42
                    vv
clus                 CLUS_1 CLUS_2 CLUS_3
  19Q LOSS MUTATED        1      0      3
  19Q LOSS WILD-TYPE     34     79     62
D29V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                0                 79
  CLUS_3                3                 62

Clustering(30) Variable = XQ LOSS MUTATION ANALYSIS
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        0      0      4      1
  XQ LOSS WILD-TYPE    147     14     23      2
D30V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0               147
  CLUS_2               0                14
  CLUS_3               4                23
  CLUS_4               1                 2
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
  XQ LOSS MUTATED        0      0      4      0      1
  XQ LOSS WILD-TYPE     46     44     57     14     19
D30V2, multiclass
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        4      1      0
  XQ LOSS WILD-TYPE     66     51     44
D30V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                66
  CLUS_2               1                51
  CLUS_3               0                44
D30V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1   4
  XQ LOSS WILD-TYPE  55 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    4
  XQ LOSS WILD-TYPE   55  106
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                55
  CLUS_2               4               106
                   vv
clus                CLUS_1 CLUS_2 CLUS_3 CLUS_4
  XQ LOSS MUTATED        0      4      1      0
  XQ LOSS WILD-TYPE     58     33     40     43
D30V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                58
  CLUS_2               4                33
  CLUS_3               1                40
  CLUS_4               0                43
                   vv
clus                CLUS_1 CLUS_2 CLUS_3
  XQ LOSS MUTATED        4      0      1
  XQ LOSS WILD-TYPE     31     79     64
D30V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                31
  CLUS_2               0                79
  CLUS_3               1                64
> q(save="no")
