[1] "ofn"        "-oTLAML-TB"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LAML-TB/22506504/LAML-TB.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/22529564/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 82 to 32."
[1]  32 191
[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 
                 5                186 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                186 
[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] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               188 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               188 
[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 
                 3                188 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                188 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                188 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                188 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5               186 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5               186 
[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] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "DAYS_TO_LAST_KNOWN_ALIVE"            
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "RACE"                                
[11] "ETHNICITY"                           

Input Data has 11 rows and 191 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "KARNOFSKY_PERFORMANCE_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 191 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     0   2
  1P GAIN WILD-TYPE  62 114
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2               176 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2               114 
$`1P GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2952 
        0.00         1.02 

$`1P GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       22.98        10.06        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 0 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.02             94.06 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            0.510            11.505 
[1] "0.0 - 1.0 (0.5)"   "0.0 - 94.1 (11.5)"
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2   1
  1P GAIN WILD-TYPE  85 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE   85  103
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                85
  MALE                 1               103
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0     3
  1P GAIN WILD-TYPE     2                        14   170
D1V4, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   3               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0   3
  1P GAIN WILD-TYPE   3 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE    3  182
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               182
[1] 2 2
[1] FALSE

Clustering(2) Variable = 4P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     2   2
  4P GAIN WILD-TYPE  60 114
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               174 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               114 
$`4P GAIN MUTATED`
TCGA-AB-2849 TCGA-AB-2855 TCGA-AB-2883 TCGA-AB-2945 
       72.99         6.97        24.00         7.99 

$`4P GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 
       14.96         2.01         7.96         2.93        12.03         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
       21.07         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             6.97              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            72.99             94.06 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           15.995            11.010 
[1] "7.0 - 73.0 (16.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.6"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   3
  4P GAIN WILD-TYPE  86 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    3
  4P GAIN WILD-TYPE   86  101
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                86
  MALE                 3               101
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0     4
  4P GAIN WILD-TYPE     2                        14   169
D2V4, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   4               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   4
  4P GAIN WILD-TYPE   3 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    4
  4P GAIN WILD-TYPE    3  181
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               181
[1] 2 2
[1] FALSE

Clustering(3) Variable = 4Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     2   2
  4Q GAIN WILD-TYPE  60 114
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               174 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               114 
$`4Q GAIN MUTATED`
TCGA-AB-2849 TCGA-AB-2855 TCGA-AB-2883 TCGA-AB-2945 
       72.99         6.97        24.00         7.99 

$`4Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 
       14.96         2.01         7.96         2.93        12.03         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
       21.07         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             6.97              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            72.99             94.06 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           15.995            11.010 
[1] "7.0 - 73.0 (16.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   3
  4Q GAIN WILD-TYPE  86 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    3
  4Q GAIN WILD-TYPE   86  101
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                86
  MALE                 3               101
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     4
  4Q GAIN WILD-TYPE     2                        14   169
D3V4, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   4               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   4
  4Q GAIN WILD-TYPE   3 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE    3  181
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               4               181
[1] 2 2
[1] FALSE

Clustering(4) Variable = 8P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     6  16
  8P GAIN WILD-TYPE  56 100
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22               156 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               16               100 
$`8P GAIN MUTATED`
TCGA-AB-2807 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2838 TCGA-AB-2861 
        5.95         0.00        27.02        31.99        12.00         0.00 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2868 TCGA-AB-2878 TCGA-AB-2883 TCGA-AB-2898 
        1.02        18.97         4.96        12.00        24.00        12.92 
TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2920 TCGA-AB-2926 
        1.94        17.00         9.01        39.98        12.03        15.02 
TCGA-AB-2935 TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-3007 
        2.01        22.98         1.02        51.98 

$`8P GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 
       26.04        84.07        18.97        31.07        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 
        1.02         7.99        12.03         1.02        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2823 TCGA-AB-2824 
        8.05         8.98         9.96        82.06         0.00         0.99 
TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 
        6.97        24.03         8.98        75.09         8.98         9.04 
TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 
       21.04        12.00         8.05        55.00        17.03         0.00 
TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 
       15.98         0.92        46.06         0.00         4.01         9.99 
TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 
       46.09        14.96        72.99         2.01         7.96         2.93 
TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 
       12.03         6.97         4.93        10.06        18.97         9.99 
TCGA-AB-2860 TCGA-AB-2862 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 
       14.04        47.01         2.01         5.03         6.05         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 
        5.03         5.03        20.98         8.98        13.02         6.97 
TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 
       20.98         8.05        12.92        12.00        24.03         7.04 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2899 TCGA-AB-2900 
        5.95         5.03         7.04         7.99        22.06         6.05 
TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
        0.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 
       38.99        26.04         0.00        29.00        39.98         2.01 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2927 TCGA-AB-2929 
        0.00         1.02         2.96         7.99         2.96         4.04 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        0.00         4.01         0.92         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
       10.06        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       69.04        15.95        27.02        18.97        61.97        62.04 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            51.98             94.06 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           12.015            10.520 
[1] "0.0 - 52.0 (12.0)" "0.0 - 94.1 (10.5)"
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6 16
  8P GAIN WILD-TYPE 81 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6   16
  8P GAIN WILD-TYPE   81   88
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               6                81
  MALE                16                88
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    21
  8P GAIN WILD-TYPE     2                        13   152
D4V4, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                13
  WHITE                                  21               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  21
  8P GAIN WILD-TYPE   2 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   21
  8P GAIN WILD-TYPE    2  164
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              21               164
[1] 2 2
[1] FALSE

Clustering(5) Variable = 8Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    6 17
  8Q GAIN WILD-TYPE 56 99
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23               155 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17                99 
$`8Q GAIN MUTATED`
TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2838 
       31.07         5.95         0.00        27.02        31.99        12.00 
TCGA-AB-2861 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2868 TCGA-AB-2878 TCGA-AB-2883 
        0.00         1.02        18.97         4.96        12.00        24.00 
TCGA-AB-2898 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2920 
       12.92         1.94        17.00         9.01        39.98        12.03 
TCGA-AB-2926 TCGA-AB-2935 TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-3007 
       15.02         2.01        22.98         1.02        51.98 

$`8Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 
       26.04        84.07        18.97        94.06         2.04         1.02 
TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 
        7.99        12.03         1.02        26.04        27.02         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 
        8.98         9.96        82.06         0.00         0.99         6.97 
TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 
       24.03         8.98        75.09         8.98         9.04        21.04 
TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 
       12.00         8.05        55.00        17.03         0.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       14.96        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 
        6.97         4.93        10.06        18.97         9.99        14.04 
TCGA-AB-2862 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 
       47.01         2.01         5.03         6.05         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 
        5.03        20.98         8.98        13.02         6.97        20.98 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 
        8.05        12.92        12.00        24.03         7.04         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2903 
        5.03         7.04         7.99        22.06         6.05         0.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 
       26.04         0.00        29.00        39.98         2.01         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        1.02         2.96         7.99         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 
        4.01         0.92         1.94         7.07         9.99        14.96 
TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2950 
        0.00        21.07         7.99         1.02        19.07        10.06 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        27.02        18.97        61.97        62.04 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 0 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            51.98             94.06 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.03             10.06 
[1] "0.0 - 52.0 (12.0)" "0.0 - 94.1 (10.1)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6 17
  8Q GAIN WILD-TYPE 81 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   17
  8Q GAIN WILD-TYPE   81   87
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6                81
  MALE                17                87
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         1    22
  8Q GAIN WILD-TYPE     2                        13   151
D5V4, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                13
  WHITE                                  22               151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1  22
  8Q GAIN WILD-TYPE   2 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   22
  8Q GAIN WILD-TYPE    2  163
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO              22               163
[1] 2 2
[1] FALSE

Clustering(6) Variable = 10Q GAIN MUTATION ANALYSIS
D6V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     1   2
  10Q GAIN WILD-TYPE  61 114
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                175 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                114 
$`10Q GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2901 TCGA-AB-2935 
        0.00         1.94         2.01 

$`10Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2903 
        7.04         7.99        12.92        22.06         6.05         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        7.99        15.02         2.96         4.04         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        0.92         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  0 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              2.01              94.06 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.94              12.00 
[1] "0.0 - 2.0 (1.9)"   "0.0 - 94.1 (12.0)"
[1] "hr=" "6.3"
D6V2, continuous
D6V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   3
  10Q GAIN WILD-TYPE  87 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE   87  101
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                0                 87
  MALE                  3                101
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         1     2
  10Q GAIN WILD-TYPE     2                        13   171
D6V4, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                 13
  WHITE                                    2                171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   3
  10Q GAIN WILD-TYPE   3 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    3
  10Q GAIN WILD-TYPE    3  182
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                3                182
[1] 2 2
[1] FALSE

Clustering(7) Variable = 11P GAIN MUTATION ANALYSIS
D7V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     1   3
  11P GAIN WILD-TYPE  61 113
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                174 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                113 
$`11P GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2838 TCGA-AB-2904 TCGA-AB-2916 
           0           12           17           29 

$`11P GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       24.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2917 TCGA-AB-2919 
        9.01        39.98        26.04         0.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
        2.96         4.04         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        1.94         7.07         9.99        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  0 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             29.00              94.06 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            14.500             10.995 
[1] "0.0 - 29.0 (14.5)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2   3
  11P GAIN WILD-TYPE  85 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    3
  11P GAIN WILD-TYPE   85  101
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 85
  MALE                  3                101
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0     5
  11P GAIN WILD-TYPE     2                        14   168
D7V4, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    5                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   4
  11P GAIN WILD-TYPE   2 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    4
  11P GAIN WILD-TYPE    2  181
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                4                181
[1] 2 2
[1] FALSE

Clustering(8) Variable = 11Q GAIN MUTATION ANALYSIS
D8V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     1   5
  11Q GAIN WILD-TYPE  61 111
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                172 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                111 
$`11Q GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2830 TCGA-AB-2838 TCGA-AB-2885 TCGA-AB-2904 TCGA-AB-2916 
        0.00         9.04        12.00         7.04        17.00        29.00 

$`11Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
       75.09         8.98        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       17.03         0.00        15.98         0.92        46.06         0.00 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        4.01         9.99        46.09        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 
        7.96         2.93        12.03         6.97         4.93        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
       18.97         9.99        14.04         0.00        47.01         1.02 
TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
       18.97         2.01         5.03         6.05         4.96         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 
        5.03         5.03        20.98         8.98        13.02         6.97 
TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
       20.98        12.00         8.05        12.92        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
       24.03         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 
       22.06         6.05         1.94         0.00        52.96        18.97 
TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 
        1.02         0.99         0.00        38.99         9.01        39.98 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 
       26.04         0.00        39.98         2.01        12.03         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 
        1.02         2.96         7.99        15.02         2.96         4.04 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        0.00         4.01         0.92         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        9.99        14.96         0.00        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
       19.07        22.98        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
        6.02        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
       28.08        34.03        15.06        37.05        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98         4.93        11.01        38.04         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        6.05         0.99        12.00        15.02        60.03        56.09 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  0 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             29.00              94.06 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             10.52              11.01 
[1] "0.0 - 29.0 (10.5)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.5"
D8V2, continuous
D8V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   4
  11Q GAIN WILD-TYPE  84 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    4
  11Q GAIN WILD-TYPE   84  100
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 84
  MALE                  4                100
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0     7
  11Q GAIN WILD-TYPE     2                        14   166
D8V4, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    7                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   6
  11Q GAIN WILD-TYPE   2 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    6
  11Q GAIN WILD-TYPE    2  179
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  2
  NOT HISPANIC OR LATINO                6                179
[1] 2 2
[1] FALSE

Clustering(9) Variable = 13Q GAIN MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     1   5
  13Q GAIN WILD-TYPE  61 111
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                172 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                111 
$`13Q GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2899 TCGA-AB-2904 TCGA-AB-2917 TCGA-AB-2933 TCGA-AB-2959 
        0.00        22.06        17.00        39.98         4.01        16.08 

$`13Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.04         7.99        12.92         6.05         1.94         0.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2919 
        9.01        39.98        26.04         0.00        29.00         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 
        2.96         4.04         0.00         0.92         2.01         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 
        7.07         9.99        14.96         0.00        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
       16.08         6.02        20.02        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
       28.08        34.03        15.06        37.05        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98         4.93        11.01        38.04         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        6.05         0.99        12.00        15.02        60.03        56.09 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  0 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             39.98              94.06 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            16.540             10.995 
[1] "0.0 - 40.0 (16.5)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.3"
D9V2, continuous
D9V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2   4
  13Q GAIN WILD-TYPE  85 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    4
  13Q GAIN WILD-TYPE   85  100
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                2                 85
  MALE                  4                100
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     6
  13Q GAIN WILD-TYPE     2                        14   167
D9V4, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    6                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0   6
  13Q GAIN WILD-TYPE   3 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    6
  13Q GAIN WILD-TYPE    3  179
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                6                179
[1] 2 2
[1] FALSE

Clustering(10) Variable = 17Q GAIN MUTATION ANALYSIS
D10V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     1   2
  17Q GAIN WILD-TYPE  61 114
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                175 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                114 
$`17Q GAIN MUTATED`
TCGA-AB-2855 TCGA-AB-2917 TCGA-AB-2933 
        6.97        39.98         4.01 

$`17Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       14.96        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       29.00         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2934 
        7.99        15.02         2.96         4.04         0.00         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              4.01               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             39.98              94.06 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              6.97              11.01 
[1] "4.0 - 40.0 (7.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1   2
  17Q GAIN WILD-TYPE  86 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    2
  17Q GAIN WILD-TYPE   86  102
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                1                 86
  MALE                  2                102
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0     3
  17Q GAIN WILD-TYPE     2                        14   170
D10V4, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    3                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0   3
  17Q GAIN WILD-TYPE   3 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    3
  17Q GAIN WILD-TYPE    3  182
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                3                182
[1] 2 2
[1] FALSE

Clustering(11) Variable = 19P GAIN MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     2   3
  19P GAIN WILD-TYPE  60 113
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                173 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                113 
$`19P GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2855 TCGA-AB-2883 TCGA-AB-2917 TCGA-AB-2956 
        0.00         6.97        24.00        39.98         6.02 

$`19P GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 
       72.99         2.01         7.96         2.93        12.03         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2919 
        9.01        39.98        26.04         0.00        29.00         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
        2.96         4.04         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        1.94         7.07         9.99        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       49.05        16.08        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  0 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             39.98              94.06 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              6.97              11.01 
[1] "0.0 - 40.0 (7.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1   4
  19P GAIN WILD-TYPE  86 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    4
  19P GAIN WILD-TYPE   86  100
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 86
  MALE                  4                100
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0     5
  19P GAIN WILD-TYPE     2                        14   168
D11V4, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    5                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   5
  19P GAIN WILD-TYPE   3 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    5
  19P GAIN WILD-TYPE    3  180
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                180
[1] 2 2
[1] FALSE

Clustering(12) Variable = 19Q GAIN MUTATION ANALYSIS
D12V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     2   3
  19Q GAIN WILD-TYPE  60 113
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 5                173 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                113 
$`19Q GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2855 TCGA-AB-2883 TCGA-AB-2917 TCGA-AB-2956 
        0.00         6.97        24.00        39.98         6.02 

$`19Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 
       72.99         2.01         7.96         2.93        12.03         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2919 
        9.01        39.98        26.04         0.00        29.00         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
        2.96         4.04         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        1.94         7.07         9.99        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       49.05        16.08        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  0 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             39.98              94.06 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              6.97              11.01 
[1] "0.0 - 40.0 (7.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1   4
  19Q GAIN WILD-TYPE  86 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    4
  19Q GAIN WILD-TYPE   86  100
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                1                 86
  MALE                  4                100
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         0     5
  19Q GAIN WILD-TYPE     2                        14   168
D12V4, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    5                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   5
  19Q GAIN WILD-TYPE   3 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    5
  19Q GAIN WILD-TYPE    3  180
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                180
[1] 2 2
[1] FALSE

Clustering(13) Variable = 21Q GAIN MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     2   5
  21Q GAIN WILD-TYPE  60 111
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                171 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                111 
$`21Q GAIN MUTATED`
TCGA-AB-2807 TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2865 TCGA-AB-2868 TCGA-AB-2883 
        5.95         1.02         8.98         2.01         4.96        24.00 
TCGA-AB-2901 
        1.94 

$`21Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 
       26.04        84.07        18.97        31.07        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 
        1.02         7.99        12.03        26.04        27.02         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.98         9.96        82.06         0.00        27.02        31.99 
TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00         0.99         6.97        24.03         8.98        75.09 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        9.04        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
        0.00        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        4.01         9.99        46.09        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 
        7.96         2.93        12.03         6.97         4.93        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
       18.97         9.99        14.04         0.00        47.01         1.02 
TCGA-AB-2864 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
       18.97         5.03         6.05         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 
       20.98         8.98        13.02         6.97        20.98        12.00 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 
        8.05        12.92        12.00        24.03         7.04         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 
       22.98        10.06         1.02        49.05        16.08         6.02 
TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 
       20.02        16.08        53.98        41.98        11.01        28.08 
TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 
       34.03        15.06        37.05        10.03        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 
       20.02         3.02        30.08         1.02        22.98        22.98 
TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
        4.93        11.01        38.04         8.98         6.97         6.05 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 
        0.99        12.00        15.02        60.03        56.09        25.02 
TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 
       59.11        50.99        51.98         1.02        57.04        41.06 
TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 
       51.98        47.05        69.04        15.95        51.98        27.02 
TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       18.97        61.97        62.04 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.02               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             24.00              94.06 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.96              12.00 
[1] "1.0 - 24.0 (5.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "2.3"
D13V2, continuous
D13V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  7
  21Q GAIN WILD-TYPE 86 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    7
  21Q GAIN WILD-TYPE   86   97
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 86
  MALE                  7                 97
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         2     6
  21Q GAIN WILD-TYPE     2                        12   167
D13V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                 12
  WHITE                                    6                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0   8
  21Q GAIN WILD-TYPE   3 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    8
  21Q GAIN WILD-TYPE    3  177
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                8                177
[1] 2 2
[1] FALSE

Clustering(14) Variable = 22Q GAIN MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     2   6
  22Q GAIN WILD-TYPE  60 110
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 8                170 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                110 
$`22Q GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2860 TCGA-AB-2868 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2920 
        0.00        14.04         4.96        17.00         1.02        12.03 
TCGA-AB-2949 TCGA-AB-2954 
       22.98        49.05 

$`22Q GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 
        4.93        10.06        18.97         9.99         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 
        1.02        18.97         2.01         5.03         6.05         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 
        5.03         5.03        20.98         8.98        13.02         6.97 
TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
       20.98        12.00         8.05        12.92        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 
       12.92        22.06         6.05         1.94         0.00        52.96 
TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 
       18.97         0.99         0.00        38.99         9.01        39.98 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2922 
       26.04         0.00        29.00        39.98         2.01         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 
        1.02         2.96         7.99        15.02         2.96         4.04 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        0.00         4.01         0.92         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        9.99        14.96         0.00        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       19.07        10.06         1.02        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  0 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             49.05              94.06 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            13.035             10.995 
[1] "0.0 - 49.0 (13.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.3"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  6
  22Q GAIN WILD-TYPE 84 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    6
  22Q GAIN WILD-TYPE   84   98
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 84
  MALE                  6                 98
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         0     9
  22Q GAIN WILD-TYPE     2                        14   164
D14V4, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    9                164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   9
  22Q GAIN WILD-TYPE   3 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    9
  22Q GAIN WILD-TYPE    3  176
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                9                176
[1] 2 2
[1] FALSE

Clustering(15) Variable = XP GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED     1   2
  XP GAIN WILD-TYPE  61 114
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                3               175 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2               114 
$`XP GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2883 TCGA-AB-2929 
        0.00        24.00         4.04 

$`XP GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
        7.99        15.02         2.96         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            24.00             94.06 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
             4.04             11.01 
[1] "0.0 - 24.0 (4.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.7"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     1   2
  XP GAIN WILD-TYPE  86 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      1    2
  XP GAIN WILD-TYPE   86  102
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               1                86
  MALE                 2               102
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       0                         0     3
  XP GAIN WILD-TYPE     2                        14   170
D15V4, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   3               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0   3
  XP GAIN WILD-TYPE   3 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0    3
  XP GAIN WILD-TYPE    3  182
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               182
[1] 2 2
[1] FALSE

Clustering(16) Variable = XQ GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     1   2
  XQ GAIN WILD-TYPE  61 114
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               175 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               114 
$`XQ GAIN MUTATED`
TCGA-AB-2820 TCGA-AB-2883 TCGA-AB-2929 
        0.00        24.00         4.04 

$`XQ GAIN WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 
       27.02         8.05         8.98         9.96        82.06        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
        7.99        15.02         2.96         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            24.00             94.06 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.04             11.01 
[1] "0.0 - 24.0 (4.0)"  "0.0 - 94.1 (11.0)"
[1] "hr=" "1.7"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1   2
  XQ GAIN WILD-TYPE  86 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    2
  XQ GAIN WILD-TYPE   86  102
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                86
  MALE                 2               102
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0     3
  XQ GAIN WILD-TYPE     2                        14   170
D16V4, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   3               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   3
  XQ GAIN WILD-TYPE   3 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    3
  XQ GAIN WILD-TYPE    3  182
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               182
[1] 2 2
[1] FALSE

Clustering(17) Variable = 3P LOSS MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  62 113
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               175 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3               113 
$`3P LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2885 TCGA-AB-2941 
        1.02         7.04         0.00 

$`3P LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.00        24.00        24.03         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        7.99        15.02         2.96         4.04         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 
        0.92         2.01         1.94         7.07         9.99        14.96 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 0 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             7.04             94.06 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.02             12.00 
[1] "0.0 - 7.0 (1.0)"   "0.0 - 94.1 (12.0)"
[1] "hr=" "6.3"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE  87 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE   87  101
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               0                87
  MALE                 3               101
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0     3
  3P LOSS WILD-TYPE     2                        14   170
D17V4, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   3               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   3
  3P LOSS WILD-TYPE   3 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    3
  3P LOSS WILD-TYPE    3  182
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               182
[1] 2 2
[1] FALSE

Clustering(18) Variable = 3Q LOSS MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE  62 113
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               175 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               113 
$`3Q LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2885 TCGA-AB-2941 
        1.02         7.04         0.00 

$`3Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.00        24.00        24.03         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        7.99        15.02         2.96         4.04         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 
        0.92         2.01         1.94         7.07         9.99        14.96 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 0 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             7.04             94.06 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.02             12.00 
[1] "0.0 - 7.0 (1.0)"   "0.0 - 94.1 (12.0)"
[1] "hr=" "6.3"
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE  87 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE   87  101
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               0                87
  MALE                 3               101
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         0     3
  3Q LOSS WILD-TYPE     2                        14   170
D18V4, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   3               170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   3
  3Q LOSS WILD-TYPE   3 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    3
  3Q LOSS WILD-TYPE    3  182
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               3               182
[1] 2 2
[1] FALSE

Clustering(19) Variable = 5Q LOSS MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     0   6
  5Q LOSS WILD-TYPE  62 110
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               172 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               110 
$`5Q LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2868 TCGA-AB-2908 
        1.02         8.98        12.00        10.06         4.96         1.02 

$`5Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
       75.09         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       17.03         0.00        15.98         0.92        46.06         0.00 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        4.01         9.99        46.09        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 
        7.96         2.93        12.03         6.97         4.93        18.97 
TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
        9.99        14.04         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        2.01         5.03         6.05         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 
       20.98         8.98        13.02         6.97        20.98        12.00 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 
        8.05        12.92        12.00        24.00        24.03         7.04 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
        5.95         5.03         7.04         7.99        12.92        22.06 
TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
        6.05         1.94         0.00        17.00        52.96        18.97 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 
        0.99         0.00        38.99         9.01        39.98        26.04 
TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 
        0.00        29.00        39.98         2.01        12.03         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 
        1.02         2.96         7.99        15.02         2.96         4.04 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        0.00         4.01         0.92         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        9.99        14.96         0.00        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
       19.07        22.98        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
        6.02        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
       28.08        34.03        15.06        37.05        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98         4.93        11.01        38.04         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        6.05         0.99        12.00        15.02        60.03        56.09 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 
       41.06        51.98        47.05        69.04        15.95        51.98 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       27.02        18.97        61.97        62.04 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.02              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            12.00             94.06 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             6.97             12.00 
[1] "1.0 - 12.0 (7.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3.1"
D19V2, continuous
D19V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    0  6
  5Q LOSS WILD-TYPE 87 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    6
  5Q LOSS WILD-TYPE   87   98
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               0                87
  MALE                 6                98
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         1     5
  5Q LOSS WILD-TYPE     2                        13   168
D19V4, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                13
  WHITE                                   5               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0   6
  5Q LOSS WILD-TYPE   3 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    6
  5Q LOSS WILD-TYPE    3  179
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               6               179
[1] 2 2
[1] FALSE

Clustering(20) Variable = 7P LOSS MUTATION ANALYSIS
D20V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     3  11
  7P LOSS WILD-TYPE  59 105
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               164 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11               105 
$`7P LOSS MUTATED`
TCGA-AB-2817 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2874 TCGA-AB-2882 TCGA-AB-2885 
        8.98        12.00        10.06        13.02        12.00         7.04 
TCGA-AB-2894 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2941 
        5.95        39.98        12.03         4.04         2.01         0.00 
TCGA-AB-2949 TCGA-AB-2952 
       22.98         1.02 

$`7P LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
       27.02         8.05         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
       18.97         9.99        14.04         0.00        47.01         1.02 
TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
       18.97         2.01         5.03         6.05         4.96         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2875 TCGA-AB-2877 
        5.03         5.03        20.98         8.98         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 
       12.00         8.05        12.92        24.00        24.03         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2895 
       10.98         9.99         0.00        31.00         6.97         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
       29.00         2.01         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 
       15.02         2.96         0.00         4.01         0.92         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        7.07         9.99        14.96        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       19.07        10.06        49.05        16.08         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0                 0 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            39.98             94.06 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            9.520            11.505 
[1] "0.0 - 40.0 (9.5)"  "0.0 - 94.1 (11.5)"
[1] "hr=" "1.7"
D20V2, continuous
D20V3, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    7 10
  7P LOSS WILD-TYPE 80 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7   10
  7P LOSS WILD-TYPE   80   94
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               7                80
  MALE                10                94
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         1    16
  7P LOSS WILD-TYPE     2                        13   157
D20V4, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                13
  WHITE                                  16               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  16
  7P LOSS WILD-TYPE   3 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   16
  7P LOSS WILD-TYPE    3  169
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              16               169
[1] 2 2
[1] FALSE

Clustering(21) Variable = 7Q LOSS MUTATION ANALYSIS
D21V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     3  14
  7Q LOSS WILD-TYPE  59 102
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               161 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               14               102 
$`7Q LOSS MUTATED`
TCGA-AB-2817 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2857 TCGA-AB-2874 TCGA-AB-2878 
        8.98         8.98        12.00        10.06        13.02        12.00 
TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2894 TCGA-AB-2915 TCGA-AB-2917 TCGA-AB-2920 
       12.00         7.04         5.95         0.00        39.98        12.03 
TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2941 TCGA-AB-2949 TCGA-AB-2952 
        4.04         2.01         0.00        22.98         1.02 

$`7Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
       27.02         8.05         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
       75.09         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       17.03         0.00        15.98         0.92        46.06         0.00 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        4.01         9.99        46.09        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 
        7.96         2.93        12.03         6.97         4.93        18.97 
TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
        9.99        14.04         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
        2.01         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 
        5.03        20.98         8.98         6.97        20.98         8.05 
TCGA-AB-2881 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.92        24.00        24.03         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
        0.00        31.00         6.97         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2922 
        9.01        39.98        26.04        29.00         2.01         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 
        1.02         2.96         7.99        15.02         2.96         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 
        4.01         0.92         1.94         7.07         9.99        14.96 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2954 
       21.07         7.99         1.02        19.07        10.06        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                 0 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            39.98             94.06 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             8.98             12.00 
[1] "0.0 - 40.0 (9.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "1.9"
D21V2, continuous
D21V3, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    9 11
  7Q LOSS WILD-TYPE 78 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9   11
  7Q LOSS WILD-TYPE   78   93
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               9                78
  MALE                11                93
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         2    18
  7Q LOSS WILD-TYPE     2                        12   155
D21V4, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                12
  WHITE                                  18               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  19
  7Q LOSS WILD-TYPE   3 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   19
  7Q LOSS WILD-TYPE    3  166
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO              19               166
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P LOSS MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     0   3
  12P LOSS WILD-TYPE  62 113
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                175 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                113 
$`12P LOSS MUTATED`
TCGA-AB-2855 TCGA-AB-2929 TCGA-AB-2941 
        6.97         4.04         0.00 

$`12P LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       14.96        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 
        2.96         7.99        15.02         2.96         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 
        0.92         2.01         1.94         7.07         9.99        14.96 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       37.05        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       30.08         1.02        22.98        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  0 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              6.97              94.06 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              4.04              12.00 
[1] "0.0 - 7.0 (4.0)"   "0.0 - 94.1 (12.0)"
[1] "hr=" "5.5"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1   3
  12P LOSS WILD-TYPE  86 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    3
  12P LOSS WILD-TYPE   86  101
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                 86
  MALE                  3                101
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0     4
  12P LOSS WILD-TYPE     2                        14   169
D22V4, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    4                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0   4
  12P LOSS WILD-TYPE   3 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    4
  12P LOSS WILD-TYPE    3  181
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                4                181
[1] 2 2
[1] FALSE

Clustering(23) Variable = 15Q LOSS MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED     1   3
  15Q LOSS WILD-TYPE  61 113
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                174 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                113 
$`15Q LOSS MUTATED`
TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2939 TCGA-AB-2955 
       10.06        14.04        14.96        16.08 

$`15Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
        2.04         1.02         7.99        12.03         1.02        26.04 
TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 
       27.02         8.05         8.98         9.96        82.06         0.00 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 
       27.02        31.99         0.00         0.99         6.97        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 
        8.98        75.09         8.98         9.04        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
        0.92        46.06         0.00         4.01         9.99        46.09 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       14.96        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 
        6.97         4.93        18.97         9.99         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       24.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        7.99        15.02         2.96         4.04         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2941 
        0.92         2.01         1.94         7.07         9.99         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
       21.07         7.99         1.02        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
        1.02        49.05         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             10.06               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             16.08              94.06 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            14.500             10.995 
[1] "10.1 - 16.1 (14.5)" "0.0 - 94.1 (11.0)" 
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2   2
  15Q LOSS WILD-TYPE  85 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    2
  15Q LOSS WILD-TYPE   85  102
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                2                 85
  MALE                  2                102
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         0     4
  15Q LOSS WILD-TYPE     2                        14   169
D23V4, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    4                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0   4
  15Q LOSS WILD-TYPE   3 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0    4
  15Q LOSS WILD-TYPE    3  181
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                4                181
[1] 2 2
[1] FALSE

Clustering(24) Variable = 16Q LOSS MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     0   4
  16Q LOSS WILD-TYPE  62 112
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                174 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                112 
$`16Q LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2857 TCGA-AB-2878 TCGA-AB-2941 
        1.02        10.06        12.00         0.00 

$`16Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
        4.93        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
        6.97        20.98         8.05        12.92        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 
        2.01         1.94         7.07         9.99        14.96        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  0 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             12.00              94.06 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             5.540             11.505 
[1] "0.0 - 12.0 (5.5)"  "0.0 - 94.1 (11.5)"
[1] "hr=" "3.2"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1   3
  16Q LOSS WILD-TYPE  86 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    3
  16Q LOSS WILD-TYPE   86  101
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                1                 86
  MALE                  3                101
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         0     4
  16Q LOSS WILD-TYPE     2                        14   169
D24V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    4                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0   4
  16Q LOSS WILD-TYPE   3 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    4
  16Q LOSS WILD-TYPE    3  181
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                4                181
[1] 2 2
[1] FALSE

Clustering(25) Variable = 17P LOSS MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     2  11
  17P LOSS WILD-TYPE  60 105
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                165 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                11                105 
$`17P LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2838 TCGA-AB-2849 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2860 
        1.02        12.00        72.99         6.97        10.06        14.04 
TCGA-AB-2908 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2941 
        1.02        39.98        12.03         4.01         2.01         0.00 
TCGA-AB-2955 
       16.08 

$`17P LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2850 
        0.00         4.01         9.99        46.09        14.96         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 
        7.96         2.93        12.03         4.93        18.97         9.99 
TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        6.05         4.96         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 
        8.98        13.02         6.97        20.98        12.00         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 
       12.92        12.00        24.00        24.03         7.04         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2909 
        1.94         0.00        17.00        52.96        18.97         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
       29.00         2.01         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2934 TCGA-AB-2936 
       15.02         2.96         4.04         0.00         0.92         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        7.07         9.99        14.96        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 
       19.07        22.98        10.06         1.02        49.05         6.02 
TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 
       20.02        16.08        53.98        41.98        11.01        28.08 
TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 
       34.03        15.06        37.05        10.03        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 
       20.02         3.02        30.08         1.02        22.98        22.98 
TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
        4.93        11.01        38.04         8.98         6.97         6.05 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 
        0.99        12.00        15.02        60.03        56.09        25.02 
TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 
       59.11        50.99        51.98         1.02        57.04        41.06 
TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 
       51.98        47.05        69.04        15.95        51.98        27.02 
TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       18.97        61.97        62.04 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  0 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             72.99              94.06 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.06              11.01 
[1] "0.0 - 73.0 (10.1)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.7"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    3 10
  17P LOSS WILD-TYPE 84 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   10
  17P LOSS WILD-TYPE   84   94
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                3                 84
  MALE                 10                 94
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         0    13
  17P LOSS WILD-TYPE     2                        14   160
D25V4, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                   13                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     0  13
  17P LOSS WILD-TYPE   3 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0   13
  17P LOSS WILD-TYPE    3  172
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO               13                172
[1] 2 2
[1] FALSE

Clustering(26) Variable = 17Q LOSS MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED     1   6
  17Q LOSS WILD-TYPE  61 110
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 7                171 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                110 
$`17Q LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2838 TCGA-AB-2849 TCGA-AB-2860 TCGA-AB-2935 TCGA-AB-2941 
        1.02        12.00        72.99        14.04         2.01         0.00 
TCGA-AB-2955 
       16.08 

$`17Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2850 
        0.00         4.01         9.99        46.09        14.96         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 
        7.96         2.93        12.03         6.97         4.93        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
        2.01         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 
        5.03        20.98         8.98        13.02         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 
       12.00         8.05        12.92        12.00        24.00        24.03 
TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
        7.04         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       22.06         6.05         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 
       39.98        26.04         0.00        29.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 
        2.96         4.04         0.00         4.01         0.92         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 
        7.07         9.99        14.96        21.07         7.99         1.02 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 
       19.07        22.98        10.06         1.02        49.05         6.02 
TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 
       20.02        16.08        53.98        41.98        11.01        28.08 
TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 
       34.03        15.06        37.05        10.03        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 
       20.02         3.02        30.08         1.02        22.98        22.98 
TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
        4.93        11.01        38.04         8.98         6.97         6.05 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 
        0.99        12.00        15.02        60.03        56.09        25.02 
TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 
       59.11        50.99        51.98         1.02        57.04        41.06 
TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 
       51.98        47.05        69.04        15.95        51.98        27.02 
TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       18.97        61.97        62.04 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  0 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             72.99              94.06 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             12.00              11.01 
[1] "0.0 - 73.0 (12.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.6"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  5
  17Q LOSS WILD-TYPE 85 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    5
  17Q LOSS WILD-TYPE   85   99
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 85
  MALE                  5                 99
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0     7
  17Q LOSS WILD-TYPE     2                        14   166
D26V4, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    7                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0   7
  17Q LOSS WILD-TYPE   3 178
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    7
  17Q LOSS WILD-TYPE    3  178
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                7                178
[1] 2 2
[1] FALSE

Clustering(27) Variable = 18P LOSS MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     0   5
  18P LOSS WILD-TYPE  62 111
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                173 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                111 
$`18P LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2885 TCGA-AB-2920 TCGA-AB-2935 
        1.02         8.98         7.04        12.03         2.01 

$`18P LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
       75.09         9.04        21.04        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        46.09        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
        2.01         7.96         2.93        12.03         6.97         4.93 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
       10.06        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
        2.01         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 
        2.96         4.04         0.00         4.01         0.92         1.94 
TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 
        7.07         9.99        14.96         0.00        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              1.02               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             12.03              94.06 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              7.04              12.00 
[1] "1.0 - 12.0 (7.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3.1"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    0  5
  18P LOSS WILD-TYPE 87 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    5
  18P LOSS WILD-TYPE   87   99
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                0                 87
  MALE                  5                 99
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         1     4
  18P LOSS WILD-TYPE     2                        13   169
D27V4, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                 13
  WHITE                                    4                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     0   5
  18P LOSS WILD-TYPE   3 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    5
  18P LOSS WILD-TYPE    3  180
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                5                180
[1] 2 2
[1] FALSE

Clustering(28) Variable = 18Q LOSS MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED     0   4
  18Q LOSS WILD-TYPE  62 112
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                174 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                112 
$`18Q LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2885 TCGA-AB-2935 TCGA-AB-2938 
        1.02         7.04         2.01         9.99 

$`18Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.00        24.00        24.03         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        7.99        15.02         2.96         4.04         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        0.92         1.94         7.07        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 
       41.98        11.01        28.08        34.03        15.06        37.05 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       10.03        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
        8.98         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              1.02               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              9.99              94.06 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             4.525             12.000 
[1] "1.0 - 10.0 (4.5)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3.7"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     0   4
  18Q LOSS WILD-TYPE  87 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    4
  18Q LOSS WILD-TYPE   87  100
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                0                 87
  MALE                  4                100
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         0     4
  18Q LOSS WILD-TYPE     2                        14   169
D28V4, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    4                169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     0   4
  18Q LOSS WILD-TYPE   3 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    4
  18Q LOSS WILD-TYPE    3  181
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                4                181
[1] 2 2
[1] FALSE

Clustering(29) Variable = 19P LOSS MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     0   2
  19P LOSS WILD-TYPE  62 114
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                176 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                114 
$`19P LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2955 
        1.02        16.08 

$`19P LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 
       22.98        10.06         1.02        49.05         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.02               0.00 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.08              94.06 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              8.55              11.01 
[1] "1.0 - 16.1 (8.5)"  "0.0 - 94.1 (11.0)"
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2   1
  19P LOSS WILD-TYPE  85 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE   85  103
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                2                 85
  MALE                  1                103
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     3
  19P LOSS WILD-TYPE     2                        14   170
D29V4, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    3                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0   3
  19P LOSS WILD-TYPE   3 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    3
  19P LOSS WILD-TYPE    3  182
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                3                182
[1] 2 2
[1] FALSE

Clustering(30) Variable = 19Q LOSS MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     0   2
  19Q LOSS WILD-TYPE  62 114
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                176 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                114 
$`19Q LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2955 
        1.02        16.08 

$`19Q LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        4.93        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 
       47.01         1.02        18.97         2.01         5.03         6.05 
TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 
        4.96         7.99         5.03         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
       13.02         6.97        20.98        12.00         8.05        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.00        24.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 
       22.98        10.06         1.02        49.05         6.02        20.02 
TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       16.08        53.98        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       15.06        37.05        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
        3.02        30.08         1.02        22.98        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 
       11.01        38.04         8.98         6.97         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
       12.00        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       50.99        51.98         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
       47.05        69.04        15.95        51.98        27.02        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.02               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             16.08              94.06 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              8.55              11.01 
[1] "1.0 - 16.1 (8.5)"  "0.0 - 94.1 (11.0)"
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2   1
  19Q LOSS WILD-TYPE  85 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   85  103
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                2                 85
  MALE                  1                103
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     2                        14   170
D30V4, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    3                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0   3
  19Q LOSS WILD-TYPE   3 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    3
  19Q LOSS WILD-TYPE    3  182
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  3
  NOT HISPANIC OR LATINO                3                182
[1] 2 2
[1] FALSE

Clustering(31) Variable = XP LOSS MUTATION ANALYSIS
D31V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED     1   4
  XP LOSS WILD-TYPE  61 112
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5               173 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                4               112 
$`XP LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2857 TCGA-AB-2885 TCGA-AB-2939 TCGA-AB-2941 
        1.02        10.06         7.04        14.96         0.00 

$`XP LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
        4.93        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2942 TCGA-AB-2945 
        2.01         1.94         7.07         9.99        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
                0                 0 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            14.96             94.06 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
             7.04             12.00 
[1] "0.0 - 15.0 (7.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "2.4"
D31V2, continuous
D31V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    0  5
  XP LOSS WILD-TYPE 87 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    5
  XP LOSS WILD-TYPE   87   99
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               0                87
  MALE                 5                99
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       0                         0     5
  XP LOSS WILD-TYPE     2                        14   168
D31V4, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   5               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0   5
  XP LOSS WILD-TYPE   3 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0    5
  XP LOSS WILD-TYPE    3  180
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               180
[1] 2 2
[1] FALSE

Clustering(32) Variable = XQ LOSS MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     1   4
  XQ LOSS WILD-TYPE  61 112
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               173 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               112 
$`XQ LOSS MUTATED`
TCGA-AB-2813 TCGA-AB-2857 TCGA-AB-2885 TCGA-AB-2939 TCGA-AB-2941 
        1.02        10.06         7.04        14.96         0.00 

$`XQ LOSS WILD-TYPE`
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       26.04        84.07        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 
        2.04         1.02         7.99        12.03        26.04        27.02 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        8.05         8.98         9.96        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 
       31.99         0.00         0.99         6.97        24.03         8.98 
TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       75.09         8.98         9.04        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
        4.93        18.97         9.99        14.04         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
        1.02        18.97         2.01         5.03         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        20.98        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2942 TCGA-AB-2945 
        2.01         1.94         7.07         9.99        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
        1.02        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       16.08         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 
       11.01        28.08        34.03        15.06        37.05        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 
       26.04         0.99        20.02         3.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        22.98         4.93        11.01        38.04         8.98 
TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        6.97         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
       56.09        25.02        59.11        50.99        51.98         1.02 
TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 
       57.04        41.06        51.98        47.05        69.04        15.95 
TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       51.98        27.02        18.97        61.97        62.04 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                 0 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            14.96             94.06 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             7.04             12.00 
[1] "0.0 - 15.0 (7.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "2.4"
D32V2, continuous
D32V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  5
  XQ LOSS WILD-TYPE 87 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    5
  XQ LOSS WILD-TYPE   87   99
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               0                87
  MALE                 5                99
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         0     5
  XQ LOSS WILD-TYPE     2                        14   168
D32V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   5               168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0   5
  XQ LOSS WILD-TYPE   3 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    5
  XQ LOSS WILD-TYPE    3  180
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               5               180
[1] 2 2
[1] FALSE
