[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/22570966/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=193, common to both=193
[1] "Reduce the number of clustering variables from 25 to 23."
[1]  23 193
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            52            141 
  FLT3 MUTATED FLT3 WILD-TYPE 
            52            141 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              48              145 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              48              145 
[1] "NPM1 MUTATION ANALYSIS"
[1] 3
  NPM1 MUTATED NPM1 WILD-TYPE 
            33            160 
  NPM1 MUTATED NPM1 WILD-TYPE 
            33            160 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            173 
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            173 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            175 
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            175 
[1] "TET2 MUTATION ANALYSIS"
[1] 3
  TET2 MUTATED TET2 WILD-TYPE 
            17            176 
  TET2 MUTATED TET2 WILD-TYPE 
            17            176 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            178 
  NRAS MUTATED NRAS WILD-TYPE 
            15            178 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           12           181 
  WT1 MUTATED WT1 WILD-TYPE 
           12           181 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             185 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             185 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             16             177 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             16             177 
[1] "CEBPA MUTATION ANALYSIS"
[1] 3
  CEBPA MUTATED CEBPA WILD-TYPE 
             13             180 
  CEBPA MUTATED CEBPA WILD-TYPE 
             13             180 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            15            178 
  TP53 MUTATED TP53 WILD-TYPE 
            15            178 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             8            185 
  KRAS MUTATED KRAS WILD-TYPE 
             8            185 
[1] "PHF6 MUTATION ANALYSIS"
[1] 3
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            187 
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            187 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             187 
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             187 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
            8           185 
  KIT MUTATED KIT WILD-TYPE 
            8           185 
[1] "RAD21 MUTATION ANALYSIS"
[1] 3
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             188 
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             188 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            190 
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            190 
[1] "SMC3 MUTATION ANALYSIS"
[1] 3
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            186 
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            186 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             188 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             188 
[1] "SMC1A MUTATION ANALYSIS"
[1] 3
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             187 
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             187 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              184 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              184 
[1] "SUZ12 MUTATION ANALYSIS"
[1] 3
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             190 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             190 
[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 193 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=61,	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=57,	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 193 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=62, 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 = FLT3 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  FLT3 MUTATED   17 30
  FLT3 WILD-TYPE 47 85
  FLT3 MUTATED FLT3 WILD-TYPE 
            47            132 
  FLT3 MUTATED FLT3 WILD-TYPE 
            30             85 
$`FLT3 MUTATED`
TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2825 TCGA-AB-2830 
       12.03        26.04         8.05         9.96         6.97         9.04 
TCGA-AB-2834 TCGA-AB-2836 TCGA-AB-2840 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2869 
        8.05        17.03         0.92         7.96         2.93         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2895 
        5.03         5.03         6.97        20.98         8.05         5.03 
TCGA-AB-2900 TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2913 TCGA-AB-2915 
        6.05        18.97         0.99         0.00        39.98         0.00 
TCGA-AB-2922 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2931 TCGA-AB-2934 
        0.00         2.96         7.99        15.02         0.00         0.92 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2957 TCGA-AB-2963 TCGA-AB-2965 
       21.07         7.99         1.02        20.02        53.98        11.01 
TCGA-AB-2970 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2986 
       10.03         3.02        30.08        22.98        16.01         6.97 
TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2998 TCGA-AB-3006 TCGA-AB-3007 
       25.02        59.11         1.02        15.95        51.98 

$`FLT3 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2813 TCGA-AB-2817 TCGA-AB-2819 
       94.06         2.04         1.02         1.02         8.98        82.06 
TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2826 
        0.00        27.02        31.99         0.00         0.99        24.03 
TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 
        8.98        75.09         8.98        21.04        12.00        14.99 
TCGA-AB-2835 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 
       55.00        12.00        15.98        46.06         0.00         7.07 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        4.01         9.99        46.09        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 
        2.01        12.03         6.97        10.06        18.97         9.99 
TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 
       14.04         0.00        47.01         1.02        18.97         2.01 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        5.03         6.05         4.96        20.98         8.98        13.02 
TCGA-AB-2876 TCGA-AB-2878 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 
       40.08        12.00        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-2894 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 
        5.95         7.04         7.99        12.92        22.06         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2908 TCGA-AB-2911 TCGA-AB-2912 
        0.00        17.00        52.96         1.02        38.99         9.01 
TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2923 
       26.04        29.00        39.98         2.01        12.03         1.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        2.96         4.04         4.01         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 
        9.99        14.96         0.00        19.07        22.98        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2959 TCGA-AB-2964 
        1.02        49.05        16.08         6.02        16.08        41.98 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       28.08        34.03        15.06        26.04         0.99        20.02 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
        1.02        22.98        22.06         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        8.98         6.05         0.99        12.00        15.02        60.03 
TCGA-AB-2992 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       56.09        50.99        51.98        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       47.05        69.04        27.02        18.97        61.97        62.04 

  FLT3 MUTATED FLT3 WILD-TYPE 
             0              0 
  FLT3 MUTATED FLT3 WILD-TYPE 
         59.11          94.06 
  FLT3 MUTATED FLT3 WILD-TYPE 
          8.05          12.92 
[1] "0.0 - 59.1 (8.1)"  "0.0 - 94.1 (12.9)"
[1] "hr=" "1.3"
D1V2, continuous
D1V3, binary
                cls
clus              0  1
  FLT3 MUTATED   26 26
  FLT3 WILD-TYPE 64 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     26   26
  FLT3 WILD-TYPE   64   77
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  FEMALE           26             64
  MALE             26             77
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLT3 MUTATED       2                         5    45
  FLT3 WILD-TYPE     0                        10   129
D1V4, multiclass
                           clus
vv                          FLT3 MUTATED FLT3 WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            5             10
  WHITE                               45            129
[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
  FLT3 MUTATED     0  52
  FLT3 WILD-TYPE   3 135
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED      0   52
  FLT3 WILD-TYPE    3  135
                        clus
vv                       FLT3 MUTATED FLT3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           52            135
[1] 2 2
[1] FALSE

Clustering(2) Variable = DNMT3A MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  DNMT3A MUTATED   10 34
  DNMT3A WILD-TYPE 54 81
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              44              135 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              34               81 
$`DNMT3A MUTATED`
TCGA-AB-2802 TCGA-AB-2809 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2822 TCGA-AB-2824 
       12.00         2.04         8.05         9.96        31.99         0.99 
TCGA-AB-2825 TCGA-AB-2830 TCGA-AB-2833 TCGA-AB-2839 TCGA-AB-2851 TCGA-AB-2853 
        6.97         9.04        14.99        15.98         7.96         2.93 
TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2867 TCGA-AB-2869 
        9.99         0.00         1.02        18.97         6.05         7.99 
TCGA-AB-2873 TCGA-AB-2884 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2898 TCGA-AB-2908 
        8.98        24.03         5.03         7.04        12.92         1.02 
TCGA-AB-2912 TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2925 TCGA-AB-2931 TCGA-AB-2934 
        9.01        29.00         2.01         7.99         0.00         0.92 
TCGA-AB-2938 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2949 TCGA-AB-2955 TCGA-AB-2965 
        9.99         7.99         1.02        22.98        16.08        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2974 TCGA-AB-2981 TCGA-AB-2987 
       28.08        34.03        15.06         3.02        16.01         6.05 
TCGA-AB-2988 TCGA-AB-2993 
        0.99        25.02 

$`DNMT3A 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-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2817 TCGA-AB-2819 
        1.02        12.03         1.02        26.04         8.98        82.06 
TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2823 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 
        0.00        27.02         0.00        24.03         8.98        75.09 
TCGA-AB-2829 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
        8.98        21.04        12.00         8.05        55.00        17.03 
TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 
       12.00         0.92        46.06         0.00         7.07         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        9.99        46.09        19.99        14.96        72.99         2.01 
TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2860 TCGA-AB-2862 
       12.03         6.97        10.06        18.97        14.04        47.01 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2868 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        2.01         5.03         4.96         5.03         5.03        20.98 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 
       13.02         6.97        40.08        20.98        12.00         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.92        12.00        24.00         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2894 TCGA-AB-2897 TCGA-AB-2899 
        9.99         0.00        31.00         5.95         7.99        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-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.99         0.00        38.99        39.98        26.04         0.00 
TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2926 
       39.98        12.03         0.00         1.02         2.96        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        2.96         4.04         4.01         2.01         1.94         7.07 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2952 
       14.96         0.00        21.07        19.07        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 
       49.05         6.02        20.02        16.08        53.98        41.98 
TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2976 TCGA-AB-2977 
       10.03        26.04         0.99        20.02        30.08         1.02 
TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
       22.98        22.06        22.98         4.93        11.01        38.04 
TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 
        8.98         6.97        12.00        15.02        60.03        56.09 
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 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
               0                0 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           34.03            94.06 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           8.515           13.020 
[1] "0.0 - 34.0 (8.5)"  "0.0 - 94.1 (13.0)"
[1] "hr=" "1.9"
D2V2, continuous
D2V3, binary
                  cls
clus                0  1
  DNMT3A MUTATED   27 21
  DNMT3A WILD-TYPE 63 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     27   21
  DNMT3A WILD-TYPE   63   82
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE             27               63
  MALE               21               82
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED       1                         5    42
  DNMT3A WILD-TYPE     1                        10   132
D2V4, multiclass
                           clus
vv                          DNMT3A MUTATED DNMT3A WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              5               10
  WHITE                                 42              132
[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
  DNMT3A MUTATED     2  46
  DNMT3A WILD-TYPE   1 141
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2   46
  DNMT3A WILD-TYPE    1  141
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  2                1
  NOT HISPANIC OR LATINO             46              141
[1] 2 2
[1] FALSE

Clustering(3) Variable = NPM1 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  NPM1 MUTATED   11 22
  NPM1 WILD-TYPE 53 93
  NPM1 MUTATED NPM1 WILD-TYPE 
            33            146 
  NPM1 MUTATED NPM1 WILD-TYPE 
            22             93 
$`NPM1 MUTATED`
TCGA-AB-2802 TCGA-AB-2812 TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2835 TCGA-AB-2839 
       12.00        12.03         0.99         6.97        55.00        15.98 
TCGA-AB-2848 TCGA-AB-2859 TCGA-AB-2869 TCGA-AB-2879 TCGA-AB-2896 TCGA-AB-2900 
       14.96         9.99         7.99         8.05         7.04         6.05 
TCGA-AB-2913 TCGA-AB-2915 TCGA-AB-2924 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2963 
       39.98         0.00         2.96         7.99         1.02        53.98 
TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2972 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2981 
       11.01        34.03         0.99         3.02        30.08        16.01 
TCGA-AB-2984 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
       38.04         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-3011 
       56.09        25.02        61.97 

$`NPM1 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-2813 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 
        2.04         1.02         1.02        26.04         8.05         8.98 
TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 
        9.96        82.06         0.00        27.02        31.99         0.00 
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-2833 TCGA-AB-2834 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2840 
       12.00        14.99         8.05        17.03        12.00         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
       46.06         0.00         7.07         4.01         9.99        46.09 
TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       19.99        72.99         2.01         7.96         2.93        12.03 
TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
        6.97        10.06        18.97        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-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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
       40.08        20.98        12.00        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-2894 TCGA-AB-2895 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
       31.00         5.95         5.03         7.99        12.92        22.06 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 
        1.94         0.00        17.00        52.96        18.97         1.02 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2916 
        0.99         0.00        38.99         9.01        26.04        29.00 
TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2925 
       39.98         2.01        12.03         0.00         1.02         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-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 
       21.07        19.07        22.98        10.06         1.02        49.05 
TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2964 TCGA-AB-2966 
       16.08         6.02        20.02        16.08        41.98        28.08 
TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2973 TCGA-AB-2977 TCGA-AB-2978 
       15.06        10.03        26.04        20.02         1.02        22.98 
TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2985 TCGA-AB-2991 
       22.06        22.98         4.93        11.01         8.98        60.03 
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-3012 
       18.97        62.04 

  NPM1 MUTATED NPM1 WILD-TYPE 
             0              0 
  NPM1 MUTATED NPM1 WILD-TYPE 
         61.97          94.06 
  NPM1 MUTATED NPM1 WILD-TYPE 
         11.01          12.00 
[1] "0.0 - 62.0 (11.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  NPM1 MUTATED   17 16
  NPM1 WILD-TYPE 73 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPM1 MUTATED     17   16
  NPM1 WILD-TYPE   73   87
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  FEMALE           17             73
  MALE             16             87
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPM1 MUTATED       0                         4    29
  NPM1 WILD-TYPE     2                        11   145
D3V4, multiclass
                           clus
vv                          NPM1 MUTATED NPM1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            4             11
  WHITE                               29            145
[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
  NPM1 MUTATED     0  33
  NPM1 WILD-TYPE   3 154
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPM1 MUTATED      0   33
  NPM1 WILD-TYPE    3  154
                        clus
vv                       NPM1 MUTATED NPM1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           33            154
[1] 2 2
[1] FALSE

Clustering(4) Variable = IDH2 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED     5  13
  IDH2 WILD-TYPE  59 102
  IDH2 MUTATED IDH2 WILD-TYPE 
            18            161 
  IDH2 MUTATED IDH2 WILD-TYPE 
            13            102 
$`IDH2 MUTATED`
TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2810 TCGA-AB-2821 TCGA-AB-2826 TCGA-AB-2850 
       18.97         5.95         1.02        27.02        24.03         2.01 
TCGA-AB-2864 TCGA-AB-2866 TCGA-AB-2874 TCGA-AB-2877 TCGA-AB-2898 TCGA-AB-2934 
       18.97         5.03        13.02        20.98        12.92         0.92 
TCGA-AB-2936 TCGA-AB-2948 TCGA-AB-2959 TCGA-AB-2966 TCGA-AB-2973 TCGA-AB-3002 
        1.94        19.07        16.08        28.08        20.02        47.05 

$`IDH2 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 
       12.00        26.04        84.07        31.07        94.06         2.04 
TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 
       12.03         1.02        26.04         8.05         8.98         9.96 
TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 
       82.06         0.00        31.99         0.00         0.99         6.97 
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-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 
       14.99         8.05        55.00        17.03        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 
        0.92        46.06         0.00         7.07         4.01         9.99 
TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2851 TCGA-AB-2853 
       46.09        19.99        14.96        72.99         7.96         2.93 
TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 
       12.03         6.97        10.06        18.97         9.99        14.04 
TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 
        0.00        47.01         1.02         2.01         6.05         4.96 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2875 
        7.99         5.03         5.03        20.98         8.98         6.97 
TCGA-AB-2876 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
       40.08        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-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2899 
       31.00         5.95         5.03         7.04         7.99        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-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-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 
       26.04         0.00        29.00        39.98         2.01        12.03 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
        0.00         1.02         2.96         7.99        15.02         2.96 
TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2937 TCGA-AB-2938 
        4.04         0.00         4.01         2.01         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2949 
       14.96         0.00        21.07         7.99         1.02        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        49.05        16.08         6.02        20.02 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 
       53.98        41.98        11.01        34.03        15.06        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
       26.04         0.99         3.02        30.08         1.02        22.98 
TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
       22.06        22.98        16.01         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-3005 TCGA-AB-3006 
        1.02        57.04        41.06        51.98        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 

  IDH2 MUTATED IDH2 WILD-TYPE 
          0.92           0.00 
  IDH2 MUTATED IDH2 WILD-TYPE 
         47.05          94.06 
  IDH2 MUTATED IDH2 WILD-TYPE 
        17.525         11.010 
[1] "0.9 - 47.0 (17.5)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
                cls
clus              0  1
  IDH2 MUTATED   10 10
  IDH2 WILD-TYPE 80 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     10   10
  IDH2 WILD-TYPE   80   93
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE           10             80
  MALE             10             93
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH2 MUTATED       0                         3    17
  IDH2 WILD-TYPE     2                        12   157
D4V4, multiclass
                           clus
vv                          IDH2 MUTATED IDH2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            3             12
  WHITE                               17            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"
D4V5, binary
                cls
clus               0   1
  IDH2 MUTATED     1  19
  IDH2 WILD-TYPE   2 168
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      1   19
  IDH2 WILD-TYPE    2  168
                        clus
vv                       IDH2 MUTATED IDH2 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           19            168
[1] 2 2
[1] FALSE

Clustering(5) Variable = IDH1 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     6  10
  IDH1 WILD-TYPE  58 105
  IDH1 MUTATED IDH1 WILD-TYPE 
            16            163 
  IDH1 MUTATED IDH1 WILD-TYPE 
            10            105 
$`IDH1 MUTATED`
TCGA-AB-2802 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2863 TCGA-AB-2867 TCGA-AB-2884 
       12.00        27.02        31.99         1.02         6.05        24.03 
TCGA-AB-2901 TCGA-AB-2919 TCGA-AB-2926 TCGA-AB-2945 TCGA-AB-2949 TCGA-AB-2977 
        1.94         2.01        15.02         7.99        22.98         1.02 
TCGA-AB-2984 TCGA-AB-2990 TCGA-AB-2992 TCGA-AB-3011 
       38.04        15.02        56.09        61.97 

$`IDH1 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-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 
        2.04         1.02        12.03         1.02        26.04         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2823 TCGA-AB-2824 
        8.98         9.96        82.06         0.00         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-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
       21.04        12.00        14.99         8.05        55.00        17.03 
TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 
       12.00        15.98         0.92        46.06         0.00         7.07 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        4.01         9.99        46.09        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         6.97        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2864 
       18.97         9.99        14.04         0.00        47.01        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        2.01         5.03         4.96         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 
       20.98         8.98        13.02         6.97        40.08        20.98 
TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2885 
       12.00         8.05        12.92        12.00        24.00         7.04 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2894 
        5.95        10.98         9.99         0.00        31.00         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-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
       29.00        39.98        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
        7.99         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-2950 TCGA-AB-2952 TCGA-AB-2954 
       21.07         1.02        19.07        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-2970 TCGA-AB-2971 
       11.01        28.08        34.03        15.06        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2978 TCGA-AB-2979 
        0.99        20.02         3.02        30.08        22.98        22.06 
TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2985 TCGA-AB-2986 
       22.98        16.01         4.93        11.01         8.98         6.97 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2991 TCGA-AB-2993 TCGA-AB-2994 
        6.05         0.99        12.00        60.03        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-3012 
       62.04 

  IDH1 MUTATED IDH1 WILD-TYPE 
          1.02           0.00 
  IDH1 MUTATED IDH1 WILD-TYPE 
         61.97          94.06 
  IDH1 MUTATED IDH1 WILD-TYPE 
         15.02          12.00 
[1] "1.0 - 62.0 (15.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                cls
clus              0  1
  IDH1 MUTATED   10  8
  IDH1 WILD-TYPE 80 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     10    8
  IDH1 WILD-TYPE   80   95
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE           10             80
  MALE              8             95
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         2    16
  IDH1 WILD-TYPE     2                        13   158
D5V4, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            2             13
  WHITE                               16            158
[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
  IDH1 MUTATED     0  18
  IDH1 WILD-TYPE   3 169
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   18
  IDH1 WILD-TYPE    3  169
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            169
[1] 2 2
[1] FALSE

Clustering(6) Variable = TET2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  TET2 MUTATED     6  10
  TET2 WILD-TYPE  58 105
  TET2 MUTATED TET2 WILD-TYPE 
            16            163 
  TET2 MUTATED TET2 WILD-TYPE 
            10            105 
$`TET2 MUTATED`
TCGA-AB-2822 TCGA-AB-2830 TCGA-AB-2845 TCGA-AB-2865 TCGA-AB-2873 TCGA-AB-2876 
       31.99         9.04         9.99         2.01         8.98        40.08 
TCGA-AB-2879 TCGA-AB-2908 TCGA-AB-2923 TCGA-AB-2937 TCGA-AB-2964 TCGA-AB-2965 
        8.05         1.02         1.02         7.07        41.98        11.01 
TCGA-AB-2971 TCGA-AB-2978 TCGA-AB-2996 TCGA-AB-3006 
       26.04        22.98        51.98        15.95 

$`TET2 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
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-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-2829 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 
        8.98        21.04        12.00        14.99         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       17.03        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        7.07         4.01        46.09        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         6.97        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-2868 TCGA-AB-2869 TCGA-AB-2870 
       18.97         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2878 
        5.03        20.98        13.02         6.97        20.98        12.00 
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-2894 TCGA-AB-2895 
       10.98         9.99         0.00        31.00         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-2909 TCGA-AB-2910 
        0.00        17.00        52.96        18.97         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-2924 TCGA-AB-2925 
       39.98         2.01        12.03         0.00         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-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        2.01         1.94         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-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2972 TCGA-AB-2973 
       28.08        34.03        15.06        10.03         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
        3.02        30.08         1.02        22.06        22.98        16.01 
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-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
       59.11        50.99         1.02        57.04        41.06        51.98 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       47.05        69.04        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  TET2 MUTATED TET2 WILD-TYPE 
          1.02           0.00 
  TET2 MUTATED TET2 WILD-TYPE 
         51.98          94.06 
  TET2 MUTATED TET2 WILD-TYPE 
          10.5           12.0 
[1] "1.0 - 52.0 (10.5)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                cls
clus              0  1
  TET2 MUTATED   10  7
  TET2 WILD-TYPE 80 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET2 MUTATED     10    7
  TET2 WILD-TYPE   80   96
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  FEMALE           10             80
  MALE              7             96
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TET2 MUTATED       0                         1    16
  TET2 WILD-TYPE     2                        14   158
D6V4, multiclass
                           clus
vv                          TET2 MUTATED TET2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1             14
  WHITE                               16            158
[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
  TET2 MUTATED     0  17
  TET2 WILD-TYPE   3 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET2 MUTATED      0   17
  TET2 WILD-TYPE    3  170
                        clus
vv                       TET2 MUTATED TET2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           17            170
[1] 2 2
[1] FALSE

Clustering(7) Variable = NRAS MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     5   8
  NRAS WILD-TYPE  59 107
  NRAS MUTATED NRAS WILD-TYPE 
            13            166 
  NRAS MUTATED NRAS WILD-TYPE 
             8            107 
$`NRAS MUTATED`
TCGA-AB-2808 TCGA-AB-2816 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2870 TCGA-AB-2892 
       94.06         8.05        12.00        15.98         5.03        31.00 
TCGA-AB-2923 TCGA-AB-2952 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2978 TCGA-AB-2984 
        1.02         1.02        34.03        15.06        22.98        38.04 
TCGA-AB-2985 
        8.98 

$`NRAS WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2817 
        2.04         1.02        12.03         1.02        26.04         8.98 
TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 
        9.96        82.06         0.00        27.02        31.99         0.00 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 
        0.99         6.97        24.03         8.98        75.09         8.98 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 
        9.04        21.04        12.00        14.99         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 
       17.03         0.92        46.06         0.00         7.07         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        9.99        46.09        19.99        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 
        7.96         2.93        12.03         6.97        10.06        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-2871 
        2.01         5.03         6.05         4.96         7.99         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 
       20.98         8.98        13.02         6.97        40.08        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-2894 
        7.04         5.95        10.98         9.99         0.00         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-2908 
        1.94         0.00        17.00        52.96        18.97         1.02 
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-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-2970 
       16.08        53.98        41.98        11.01        28.08        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-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2986 
       22.06        22.98        16.01         4.93        11.01         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 

  NRAS MUTATED NRAS WILD-TYPE 
          1.02           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
         94.06          84.07 
  NRAS MUTATED NRAS WILD-TYPE 
         15.06          12.00 
[1] "1.0 - 94.1 (15.1)" "0.0 - 84.1 (12.0)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                cls
clus              0  1
  NRAS MUTATED    7  8
  NRAS WILD-TYPE 83 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      7    8
  NRAS WILD-TYPE   83   95
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            7             83
  MALE              8             95
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         0    15
  NRAS WILD-TYPE     2                        15   159
D7V4, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                               15            159
[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
  NRAS MUTATED     0  15
  NRAS WILD-TYPE   3 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   15
  NRAS WILD-TYPE    3  172
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           15            172
[1] 2 2
[1] FALSE

Clustering(8) Variable = WT1 MUTATION ANALYSIS
D8V1, survival
               sevent
clus2             0   1
  WT1 MUTATED     4   7
  WT1 WILD-TYPE  60 108
  WT1 MUTATED WT1 WILD-TYPE 
           11           168 
  WT1 MUTATED WT1 WILD-TYPE 
            7           108 
$`WT1 MUTATED`
TCGA-AB-2839 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2874 TCGA-AB-2905 TCGA-AB-2913 
       15.98         4.01        46.09        13.02        52.96        39.98 
TCGA-AB-2919 TCGA-AB-2970 TCGA-AB-2976 TCGA-AB-2989 TCGA-AB-3009 
        2.01        10.03        30.08        12.00        18.97 

$`WT1 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
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-2833 
       75.09         8.98         9.04        21.04        12.00        14.99 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 
        8.05        55.00        17.03        12.00         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2845 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        0.00         7.07         9.99        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         6.97        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-2875 TCGA-AB-2876 
        5.03         5.03        20.98         8.98         6.97        40.08 
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-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
       31.00         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-2906 
       22.06         6.05         1.94         0.00        17.00        18.97 
TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2914 
        1.02         0.99         0.00        38.99         9.01        26.04 
TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
        0.00        29.00        39.98        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-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       34.03        15.06        26.04         0.99        20.02         3.02 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 
        1.02        22.98        22.06        22.98        16.01         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-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-3011 TCGA-AB-3012 
       69.04        15.95        51.98        27.02        61.97        62.04 

  WT1 MUTATED WT1 WILD-TYPE 
         2.01          0.00 
  WT1 MUTATED WT1 WILD-TYPE 
        52.96         94.06 
  WT1 MUTATED WT1 WILD-TYPE 
       15.980        11.505 
[1] "2.0 - 53.0 (16.0)" "0.0 - 94.1 (11.5)"
[1] "hr=" "1.2"
D8V2, continuous
D8V3, binary
               cls
clus             0  1
  WT1 MUTATED    5  7
  WT1 WILD-TYPE 85 96
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      5    7
  WT1 WILD-TYPE   85   96
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  FEMALE           5            85
  MALE             7            96
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WT1 MUTATED       0                         0    11
  WT1 WILD-TYPE     2                        15   163
D8V4, multiclass
                           clus
vv                          WT1 MUTATED WT1 WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0            15
  WHITE                              11           163
[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
  WT1 MUTATED     1  10
  WT1 WILD-TYPE   2 177
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      1   10
  WT1 WILD-TYPE    2  177
                        clus
vv                       WT1 MUTATED WT1 WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          10           177
[1] 2 2
[1] FALSE

Clustering(9) Variable = U2AF1 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  U2AF1 MUTATED     1   7
  U2AF1 WILD-TYPE  63 108
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             171 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              7             108 
$`U2AF1 MUTATED`
TCGA-AB-2821 TCGA-AB-2843 TCGA-AB-2847 TCGA-AB-2861 TCGA-AB-2882 TCGA-AB-2912 
       27.02         7.07        19.99         0.00        12.00         9.01 
TCGA-AB-2968 TCGA-AB-2996 
       15.06        51.98 

$`U2AF1 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2822 
        8.05         8.98         9.96        82.06         0.00        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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        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-2857 
        2.01         7.96         2.93        12.03         6.97        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99        14.04        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-2876 
        5.03        20.98         8.98        13.02         6.97        40.08 
TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2883 TCGA-AB-2884 
       20.98        12.00         8.05        12.92        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-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-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2913 TCGA-AB-2914 
        1.02         0.99         0.00        38.99        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       28.08        34.03        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 
        3.02        30.08         1.02        22.98        22.06        22.98 
TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       16.01         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-2998 TCGA-AB-2999 TCGA-AB-3000 
       25.02        59.11        50.99         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 

  U2AF1 MUTATED U2AF1 WILD-TYPE 
              0               0 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          51.98           94.06 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          13.53           12.00 
[1] "0.0 - 52.0 (13.5)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.3"
D9V2, continuous
D9V3, binary
                 cls
clus               0  1
  U2AF1 MUTATED    1  7
  U2AF1 WILD-TYPE 89 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      1    7
  U2AF1 WILD-TYPE   89   96
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  FEMALE             1              89
  MALE               7              96
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  U2AF1 MUTATED       0                         0     8
  U2AF1 WILD-TYPE     2                        15   166
D9V4, multiclass
                           clus
vv                          U2AF1 MUTATED U2AF1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0              15
  WHITE                                 8             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"
D9V5, binary
                 cls
clus                0   1
  U2AF1 MUTATED     0   7
  U2AF1 WILD-TYPE   3 180
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      0    7
  U2AF1 WILD-TYPE    3  180
                        clus
vv                       U2AF1 MUTATED U2AF1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7             180
[1] 2 2
[1] FALSE

Clustering(10) Variable = RUNX1 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED     2  13
  RUNX1 WILD-TYPE  62 102
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             15             164 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             13             102 
$`RUNX1 MUTATED`
TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2821 TCGA-AB-2850 TCGA-AB-2865 TCGA-AB-2890 
       18.97         5.95        27.02         2.01         2.01         0.00 
TCGA-AB-2899 TCGA-AB-2912 TCGA-AB-2927 TCGA-AB-2933 TCGA-AB-2936 TCGA-AB-2959 
       22.06         9.01         2.96         4.01         1.94        16.08 
TCGA-AB-2970 TCGA-AB-2978 TCGA-AB-3009 
       10.03        22.98        18.97 

$`RUNX1 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 
       12.00        26.04        84.07        31.07        94.06         2.04 
TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 TCGA-AB-2817 
        1.02        12.03         1.02        26.04         8.05         8.98 
TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 
        9.96        82.06         0.00        31.99         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-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
       21.04        12.00        14.99         8.05        55.00        17.03 
TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 
       12.00        15.98         0.92        46.06         0.00         7.07 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        4.01         9.99        46.09        19.99        14.96        72.99 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 
        7.96         2.93        12.03         6.97        10.06        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-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        5.03         6.05         4.96         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 
       20.98         8.98        13.02         6.97        40.08        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-2892 TCGA-AB-2894 
        7.04         5.95        10.98         9.99        31.00         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2900 TCGA-AB-2901 
        5.03         7.04         7.99        12.92         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-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
        0.00        38.99        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-2929 TCGA-AB-2931 TCGA-AB-2934 TCGA-AB-2935 
        7.99        15.02         4.04         0.00         0.92         2.01 
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-2971 TCGA-AB-2972 TCGA-AB-2973 
       28.08        34.03        15.06        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
        3.02        30.08         1.02        22.06        22.98        16.01 
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-3011 TCGA-AB-3012 
       61.97        62.04 

  RUNX1 MUTATED RUNX1 WILD-TYPE 
              0               0 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
          27.02           94.06 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
           9.01           12.00 
[1] "0.0 - 27.0 (9.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "1.9"
D10V2, continuous
D10V3, binary
                 cls
clus               0  1
  RUNX1 MUTATED    7  9
  RUNX1 WILD-TYPE 83 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      7    9
  RUNX1 WILD-TYPE   83   94
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  FEMALE             7              83
  MALE               9              94
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1 MUTATED       0                         1    14
  RUNX1 WILD-TYPE     2                        14   160
D10V4, multiclass
                           clus
vv                          RUNX1 MUTATED RUNX1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                14             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"
D10V5, binary
                 cls
clus                0   1
  RUNX1 MUTATED     0  15
  RUNX1 WILD-TYPE   3 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      0   15
  RUNX1 WILD-TYPE    3  172
                        clus
vv                       RUNX1 MUTATED RUNX1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            15             172
[1] 2 2
[1] FALSE

Clustering(11) Variable = CEBPA MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  CEBPA MUTATED     4   7
  CEBPA WILD-TYPE  60 108
  CEBPA MUTATED CEBPA WILD-TYPE 
             11             168 
  CEBPA MUTATED CEBPA WILD-TYPE 
              7             108 
$`CEBPA MUTATED`
TCGA-AB-2808 TCGA-AB-2839 TCGA-AB-2845 TCGA-AB-2863 TCGA-AB-2874 TCGA-AB-2900 
       94.06        15.98         9.99         1.02        13.02         6.05 
TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2979 TCGA-AB-3000 TCGA-AB-3008 
        1.02        16.08        22.06        41.06        27.02 

$`CEBPA WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 
        2.04         1.02        12.03         1.02        26.04         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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       55.00        17.03        12.00         0.92        46.06         0.00 
TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        7.07         4.01        46.09        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         6.97        10.06 
TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2864 
       18.97         9.99        14.04         0.00        47.01        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-2876 TCGA-AB-2877 
        5.03        20.98         8.98         6.97        40.08        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-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-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 
        1.94         0.00        17.00        52.96        18.97         1.02 
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-2954 TCGA-AB-2956 TCGA-AB-2957 
       19.07        22.98        10.06        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       15.06        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 
       30.08         1.02        22.98        22.98        16.01         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-3001 TCGA-AB-3002 
       50.99        51.98         1.02        57.04        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       69.04        15.95        51.98        18.97        61.97        62.04 

  CEBPA MUTATED CEBPA WILD-TYPE 
           1.02            0.00 
  CEBPA MUTATED CEBPA WILD-TYPE 
          94.06           84.07 
  CEBPA MUTATED CEBPA WILD-TYPE 
          15.98           12.00 
[1] "1.0 - 94.1 (16.0)" "0.0 - 84.1 (12.0)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                 cls
clus               0  1
  CEBPA MUTATED    5  8
  CEBPA WILD-TYPE 85 95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED      5    8
  CEBPA WILD-TYPE   85   95
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  FEMALE             5              85
  MALE               8              95
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEBPA MUTATED       0                         1    12
  CEBPA WILD-TYPE     2                        14   162
D11V4, multiclass
                           clus
vv                          CEBPA MUTATED CEBPA WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                12             162
[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
  CEBPA MUTATED     0  13
  CEBPA WILD-TYPE   3 174
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED      0   13
  CEBPA WILD-TYPE    3  174
                        clus
vv                       CEBPA MUTATED CEBPA WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             174
[1] 2 2
[1] FALSE

Clustering(12) Variable = TP53 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     0  14
  TP53 WILD-TYPE  64 101
  TP53 MUTATED TP53 WILD-TYPE 
            14            165 
  TP53 MUTATED TP53 WILD-TYPE 
            14            101 
$`TP53 MUTATED`
TCGA-AB-2813 TCGA-AB-2820 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2860 TCGA-AB-2868 
        1.02         0.00         8.98        12.00        14.04         4.96 
TCGA-AB-2878 TCGA-AB-2885 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2935 TCGA-AB-2938 
       12.00         7.04        17.00         1.02         2.01         9.99 
TCGA-AB-2941 TCGA-AB-2952 
        0.00         1.02 

$`TP53 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2816 
       94.06         2.04         1.02        12.03        26.04         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 
        8.98         9.96        82.06        27.02        31.99         0.00 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2830 
        0.99         6.97        24.03         8.98        75.09         9.04 
TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
       21.04        12.00        14.99         8.05        55.00        17.03 
TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 
       15.98         0.92        46.06         0.00         7.07         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 
        9.99        46.09        19.99        14.96        72.99         2.01 
TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 
        7.96         2.93        12.03         6.97        10.06        18.97 
TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 
        9.99         0.00        47.01         1.02        18.97         2.01 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        5.03         6.05         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2879 
        8.98        13.02         6.97        40.08        20.98         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 
       12.92        12.00        24.00        24.03         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        9.99         0.00        31.00         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-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       52.96        18.97         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-2939 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
        7.07        14.96        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       15.06        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
       30.08         1.02        22.98        22.06        22.98        16.01 
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 

  TP53 MUTATED TP53 WILD-TYPE 
             0              0 
  TP53 MUTATED TP53 WILD-TYPE 
         17.00          94.06 
  TP53 MUTATED TP53 WILD-TYPE 
          6.00          12.03 
[1] "0.0 - 17.0 (6.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "3.6"
D12V2, continuous
D12V3, binary
                cls
clus              0  1
  TP53 MUTATED    4 11
  TP53 WILD-TYPE 86 92
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   11
  TP53 WILD-TYPE   86   92
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            4             86
  MALE             11             92
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         1    14
  TP53 WILD-TYPE     2                        14   160
D12V4, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1             14
  WHITE                               14            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"
D12V5, binary
                cls
clus               0   1
  TP53 MUTATED     0  15
  TP53 WILD-TYPE   3 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   15
  TP53 WILD-TYPE    3  172
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           15            172
[1] 2 2
[1] FALSE

Clustering(13) Variable = KRAS MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     1   7
  KRAS WILD-TYPE  63 108
  KRAS MUTATED KRAS WILD-TYPE 
             8            171 
  KRAS MUTATED KRAS WILD-TYPE 
             7            108 
$`KRAS MUTATED`
TCGA-AB-2826 TCGA-AB-2861 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2917 TCGA-AB-2929 
       24.03         0.00        18.97         2.01        39.98         4.04 
TCGA-AB-2966 TCGA-AB-2987 
       28.08         6.05 

$`KRAS WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
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-2827 TCGA-AB-2828 
       31.99         0.00         0.99         6.97         8.98        75.09 
TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
        0.00         7.07         4.01         9.99        46.09        19.99 
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-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2862 
        6.97        10.06        18.97         9.99        14.04        47.01 
TCGA-AB-2863 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
        1.02         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-2876 
        5.03        20.98         8.98        13.02         6.97        40.08 
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-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
       31.00         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-2919 TCGA-AB-2920 
       39.98        26.04         0.00        29.00         2.01        12.03 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
        0.00         1.02         2.96         7.99        15.02         2.96 
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-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       34.03        15.06        10.03        26.04         0.99        20.02 
TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 
        3.02        30.08         1.02        22.98        22.06        22.98 
TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       16.01         4.93        11.01        38.04         8.98         6.97 
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 

  KRAS MUTATED KRAS WILD-TYPE 
             0              0 
  KRAS MUTATED KRAS WILD-TYPE 
         39.98          94.06 
  KRAS MUTATED KRAS WILD-TYPE 
         12.51          12.00 
[1] "0.0 - 40.0 (12.5)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.5"
D13V2, continuous
D13V3, binary
                cls
clus               0   1
  KRAS MUTATED     6   2
  KRAS WILD-TYPE  84 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6    2
  KRAS WILD-TYPE   84  101
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            6             84
  MALE              2            101
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     8
  KRAS WILD-TYPE     2                        15   166
D13V4, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                8            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"
D13V5, binary
                cls
clus               0   1
  KRAS MUTATED     1   7
  KRAS WILD-TYPE   2 180
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    7
  KRAS WILD-TYPE    2  180
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            7            180
[1] 2 2
[1] FALSE

Clustering(14) Variable = PHF6 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  PHF6 MUTATED     1   5
  PHF6 WILD-TYPE  63 110
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            173 
  PHF6 MUTATED PHF6 WILD-TYPE 
             5            110 
$`PHF6 MUTATED`
TCGA-AB-2804 TCGA-AB-2855 TCGA-AB-2912 TCGA-AB-2959 TCGA-AB-2976 TCGA-AB-3009 
       84.07         6.97         9.01        16.08        30.08        18.97 

$`PHF6 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 
       12.00        26.04        18.97        31.07         5.95        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 
        2.04         1.02        12.03         1.02        26.04         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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
        0.00         7.07         4.01         9.99        46.09        19.99 
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-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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
        6.97        40.08        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-2894 TCGA-AB-2895 TCGA-AB-2896 
        9.99         0.00        31.00         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-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
       38.99        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-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-2963 
        1.02        49.05        16.08         6.02        20.02        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 
       41.98        11.01        28.08        34.03        15.06        10.03 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2977 TCGA-AB-2978 
       26.04         0.99        20.02         3.02         1.02        22.98 
TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 
       22.06        22.98        16.01         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-3011 TCGA-AB-3012 
       15.95        51.98        27.02        61.97        62.04 

  PHF6 MUTATED PHF6 WILD-TYPE 
          6.97           0.00 
  PHF6 MUTATED PHF6 WILD-TYPE 
         84.07          94.06 
  PHF6 MUTATED PHF6 WILD-TYPE 
        17.525         12.000 
[1] "7.0 - 84.1 (17.5)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                cls
clus              0  1
  PHF6 MUTATED    0  6
  PHF6 WILD-TYPE 90 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF6 MUTATED      0    6
  PHF6 WILD-TYPE   90   97
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  FEMALE            0             90
  MALE              6             97
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF6 MUTATED       0                         0     5
  PHF6 WILD-TYPE     2                        15   169
D14V4, multiclass
                           clus
vv                          PHF6 MUTATED PHF6 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                5            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"
D14V5, binary
                cls
clus               0   1
  PHF6 MUTATED     0   5
  PHF6 WILD-TYPE   3 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF6 MUTATED      0    5
  PHF6 WILD-TYPE    3  182
                        clus
vv                       PHF6 MUTATED PHF6 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5            182
[1] 2 2
[1] FALSE

Clustering(15) Variable = STAG2 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     4   2
  STAG2 WILD-TYPE  60 113
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             173 
  STAG2 MUTATED STAG2 WILD-TYPE 
              2             113 
$`STAG2 MUTATED`
TCGA-AB-2850 TCGA-AB-2871 TCGA-AB-2913 TCGA-AB-2964 TCGA-AB-2972 TCGA-AB-2978 
        2.01         5.03        39.98        41.98         0.99        22.98 

$`STAG2 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
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-2833 
       75.09         8.98         9.04        21.04        12.00        14.99 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
        8.05        55.00        17.03        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 
       46.06         0.00         7.07         4.01         9.99        46.09 
TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 
       19.99        14.96        72.99         7.96         2.93        12.03 
TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        6.97        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-2872 TCGA-AB-2873 TCGA-AB-2874 
        4.96         7.99         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
        6.97        40.08        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-2894 TCGA-AB-2895 TCGA-AB-2896 
        9.99         0.00        31.00         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-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
       38.99         9.01        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-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-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 
       53.98        11.01        28.08        34.03        15.06        10.03 
TCGA-AB-2971 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 
       26.04        20.02         3.02        30.08         1.02        22.06 
TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        16.01         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 

  STAG2 MUTATED STAG2 WILD-TYPE 
           0.99            0.00 
  STAG2 MUTATED STAG2 WILD-TYPE 
          41.98           94.06 
  STAG2 MUTATED STAG2 WILD-TYPE 
         14.005          12.000 
[1] "1.0 - 42.0 (14.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "2"  
D15V2, continuous
D15V3, binary
                 cls
clus                0   1
  STAG2 MUTATED     4   2
  STAG2 WILD-TYPE  86 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      4    2
  STAG2 WILD-TYPE   86  101
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             4              86
  MALE               2             101
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED       0                         2     4
  STAG2 WILD-TYPE     2                        13   170
D15V4, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2              13
  WHITE                                 4             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
  STAG2 MUTATED     0   6
  STAG2 WILD-TYPE   3 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    6
  STAG2 WILD-TYPE    3  181
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             181
[1] 2 2
[1] FALSE

Clustering(16) Variable = KIT MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  KIT MUTATED     4   4
  KIT WILD-TYPE  60 111
  KIT MUTATED KIT WILD-TYPE 
            8           171 
  KIT MUTATED KIT WILD-TYPE 
            4           111 
$`KIT MUTATED`
TCGA-AB-2819 TCGA-AB-2843 TCGA-AB-2846 TCGA-AB-2881 TCGA-AB-2888 TCGA-AB-2937 
       82.06         7.07        46.09        12.92        10.98         7.07 
TCGA-AB-2939 TCGA-AB-2945 
       14.96         7.99 

$`KIT WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.05         8.98         9.96         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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        0.00         4.01         9.99        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         6.97        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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2882 TCGA-AB-2883 
       40.08        20.98        12.00         8.05        12.00        24.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
       24.03         7.04         5.95         9.99         0.00        31.00 
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-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-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 
       26.04         0.00        29.00        39.98         2.01        12.03 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
        0.00         1.02         2.96         7.99        15.02         2.96 
TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 
        4.04         0.00         4.01         0.92         2.01         1.94 
TCGA-AB-2938 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
        9.99         0.00        21.07         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       15.06        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
       30.08         1.02        22.98        22.06        22.98        16.01 
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 

  KIT MUTATED KIT WILD-TYPE 
         7.07          0.00 
  KIT MUTATED KIT WILD-TYPE 
        82.06         94.06 
  KIT MUTATED KIT WILD-TYPE 
        11.95         12.00 
[1] "7.1 - 82.1 (11.9)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.4"
D16V2, continuous
D16V3, binary
               cls
clus              0   1
  KIT MUTATED     5   3
  KIT WILD-TYPE  85 100
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      5    3
  KIT WILD-TYPE   85  100
        clus
vv       KIT MUTATED KIT WILD-TYPE
  FEMALE           5            85
  MALE             3           100
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIT MUTATED       0                         0     8
  KIT WILD-TYPE     2                        15   166
D16V4, multiclass
                           clus
vv                          KIT MUTATED KIT WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0            15
  WHITE                               8           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"
D16V5, binary
               cls
clus              0   1
  KIT MUTATED     0   8
  KIT WILD-TYPE   3 179
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      0    8
  KIT WILD-TYPE    3  179
                        clus
vv                       KIT MUTATED KIT WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           8           179
[1] 2 2
[1] FALSE

Clustering(17) Variable = RAD21 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  RAD21 MUTATED     2   2
  RAD21 WILD-TYPE  62 113
  RAD21 MUTATED RAD21 WILD-TYPE 
              4             175 
  RAD21 MUTATED RAD21 WILD-TYPE 
              2             113 
$`RAD21 MUTATED`
TCGA-AB-2818 TCGA-AB-2886 TCGA-AB-2967 TCGA-AB-2986 
        9.96         5.95        34.03         6.97 

$`RAD21 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.05         8.98        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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
        0.00         7.07         4.01         9.99        46.09        19.99 
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-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        6.97        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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 
       13.02         6.97        40.08        20.98        12.00         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2888 
       12.92        12.00        24.00        24.03         7.04        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        9.99         0.00        31.00         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-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
        0.00        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        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-2968 
       16.08        53.98        41.98        11.01        28.08        15.06 
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-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 
        1.02        22.98        22.06        22.98        16.01         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       11.01        38.04         8.98         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 

  RAD21 MUTATED RAD21 WILD-TYPE 
           5.95            0.00 
  RAD21 MUTATED RAD21 WILD-TYPE 
          34.03           94.06 
  RAD21 MUTATED RAD21 WILD-TYPE 
          8.465          12.000 
[1] "6.0 - 34.0 (8.5)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
                 cls
clus                0   1
  RAD21 MUTATED     2   3
  RAD21 WILD-TYPE  88 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED      2    3
  RAD21 WILD-TYPE   88  100
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  FEMALE             2              88
  MALE               3             100
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAD21 MUTATED       1                         1     3
  RAD21 WILD-TYPE     1                        14   171
D17V4, multiclass
                           clus
vv                          RAD21 MUTATED RAD21 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                 3             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"
D17V5, binary
                 cls
clus                0   1
  RAD21 MUTATED     0   5
  RAD21 WILD-TYPE   3 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED      0    5
  RAD21 WILD-TYPE    3  182
                        clus
vv                       RAD21 MUTATED RAD21 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5             182
[1] 2 2
[1] FALSE

Clustering(18) Variable = EZH2 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED     0   2
  EZH2 WILD-TYPE  64 113
  EZH2 MUTATED EZH2 WILD-TYPE 
             2            177 
  EZH2 MUTATED EZH2 WILD-TYPE 
             2            113 
$`EZH2 MUTATED`
TCGA-AB-2817 TCGA-AB-2865 
        8.98         2.01 

$`EZH2 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        8.05         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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
        0.00         7.07         4.01         9.99        46.09        19.99 
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-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        6.97        10.06        18.97         9.99        14.04         0.00 
TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
       47.01         1.02        18.97         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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 
        6.97        40.08        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-2894 TCGA-AB-2895 TCGA-AB-2896 
        9.99         0.00        31.00         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-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 
        0.00        21.07         7.99         1.02        19.07        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       15.06        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
       30.08         1.02        22.98        22.06        22.98        16.01 
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 

  EZH2 MUTATED EZH2 WILD-TYPE 
          2.01           0.00 
  EZH2 MUTATED EZH2 WILD-TYPE 
          8.98          94.06 
  EZH2 MUTATED EZH2 WILD-TYPE 
         5.495         12.000 
[1] "2.0 - 9.0 (5.5)"   "0.0 - 94.1 (12.0)"
[1] "Remove cluster labels:" "EZH2 MUTATED"          
D18V2, continuous
D18V3, binary
                cls
clus               0   1
  EZH2 MUTATED     1   2
  EZH2 WILD-TYPE  89 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      1    2
  EZH2 WILD-TYPE   89  101
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  FEMALE            1             89
  MALE              2            101
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EZH2 MUTATED       0                         0     3
  EZH2 WILD-TYPE     2                        15   171
D18V4, multiclass
                           clus
vv                          EZH2 MUTATED EZH2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                3            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"
D18V5, binary
                cls
clus               0   1
  EZH2 MUTATED     0   3
  EZH2 WILD-TYPE   3 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      0    3
  EZH2 WILD-TYPE    3  184
                        clus
vv                       EZH2 MUTATED EZH2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            184
[1] 2 2
[1] FALSE

Clustering(19) Variable = SMC3 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  SMC3 MUTATED     1   6
  SMC3 WILD-TYPE  63 109
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            172 
  SMC3 MUTATED SMC3 WILD-TYPE 
             6            109 
$`SMC3 MUTATED`
TCGA-AB-2839 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2908 TCGA-AB-2912 TCGA-AB-2950 
       15.98         7.96         2.93         1.02         9.01        10.06 
TCGA-AB-2993 
       25.02 

$`SMC3 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
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-2833 
       75.09         8.98         9.04        21.04        12.00        14.99 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 
        8.05        55.00        17.03        12.00         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
        0.00         7.07         4.01         9.99        46.09        19.99 
TCGA-AB-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
       14.96        72.99         2.01        12.03         6.97        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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
       40.08        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-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
        0.00        31.00         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-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2913 
       52.96        18.97         0.99         0.00        38.99        39.98 
TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 
       26.04         0.00        29.00        39.98         2.01        12.03 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
        0.00         1.02         2.96         7.99        15.02         2.96 
TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 
        4.04         0.00         4.01         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-2952 TCGA-AB-2954 TCGA-AB-2955 
        1.02        19.07        22.98         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-2970 TCGA-AB-2971 TCGA-AB-2972 
       28.08        34.03        15.06        10.03        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 
       20.02         3.02        30.08         1.02        22.98        22.06 
TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        16.01         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-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 
       56.09        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 

  SMC3 MUTATED SMC3 WILD-TYPE 
          1.02           0.00 
  SMC3 MUTATED SMC3 WILD-TYPE 
         25.02          94.06 
  SMC3 MUTATED SMC3 WILD-TYPE 
          9.01          12.00 
[1] "1.0 - 25.0 (9.0)"  "0.0 - 94.1 (12.0)"
[1] "hr=" "1.9"
D19V2, continuous
D19V3, binary
                cls
clus               0   1
  SMC3 MUTATED     4   3
  SMC3 WILD-TYPE  86 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      4    3
  SMC3 WILD-TYPE   86  100
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  FEMALE            4             86
  MALE              3            100
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMC3 MUTATED       0                         0     7
  SMC3 WILD-TYPE     2                        15   167
D19V4, multiclass
                           clus
vv                          SMC3 MUTATED SMC3 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                7            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"
D19V5, binary
                cls
clus               0   1
  SMC3 MUTATED     0   7
  SMC3 WILD-TYPE   3 180
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      0    7
  SMC3 WILD-TYPE    3  180
                        clus
vv                       SMC3 MUTATED SMC3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            180
[1] 2 2
[1] FALSE

Clustering(20) Variable = ASXL1 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED     0   4
  ASXL1 WILD-TYPE  64 111
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              4             175 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              4             111 
$`ASXL1 MUTATED`
TCGA-AB-2807 TCGA-AB-2821 TCGA-AB-2864 TCGA-AB-2927 
        5.95        27.02        18.97         2.96 

$`ASXL1 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2808 
       12.00        26.04        84.07        18.97        31.07        94.06 
TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 
        2.04         1.02        12.03         1.02        26.04         8.05 
TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2822 TCGA-AB-2823 
        8.98         9.96        82.06         0.00        31.99         0.00 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 
        0.99         6.97        24.03         8.98        75.09         8.98 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 
        9.04        21.04        12.00        14.99         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       17.03        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 
        7.07         4.01         9.99        46.09        19.99        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-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-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
        1.02         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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
       40.08        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-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
        0.00        31.00         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-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
       15.02         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-2970 
       41.98        11.01        28.08        34.03        15.06        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-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 
       22.98        22.06        22.98        16.01         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 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           2.96            0.00 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          27.02           94.06 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
          12.46           12.00 
[1] "3.0 - 27.0 (12.5)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.7"
D20V2, continuous
D20V3, binary
                 cls
clus                0   1
  ASXL1 MUTATED     3   2
  ASXL1 WILD-TYPE  87 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      3    2
  ASXL1 WILD-TYPE   87  101
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE             3              87
  MALE               2             101
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED       0                         0     5
  ASXL1 WILD-TYPE     2                        15   169
D20V4, multiclass
                           clus
vv                          ASXL1 MUTATED ASXL1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0              15
  WHITE                                 5             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"
D20V5, binary
                 cls
clus                0   1
  ASXL1 MUTATED     1   4
  ASXL1 WILD-TYPE   2 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      1    4
  ASXL1 WILD-TYPE    2  183
                        clus
vv                       ASXL1 MUTATED ASXL1 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             4             183
[1] 2 2
[1] FALSE

Clustering(21) Variable = SMC1A MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  SMC1A MUTATED     0   6
  SMC1A WILD-TYPE  64 109
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             173 
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             109 
$`SMC1A MUTATED`
TCGA-AB-2822 TCGA-AB-2824 TCGA-AB-2844 TCGA-AB-2858 TCGA-AB-2900 TCGA-AB-2963 
       31.99         0.99         4.01        18.97         6.05        53.98 

$`SMC1A WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
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-2823 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 
        0.00         6.97        24.03         8.98        75.09         8.98 
TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 
        9.04        21.04        12.00        14.99         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       17.03        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-2843 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
        7.07         9.99        46.09        19.99        14.96        72.99 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
        2.01         7.96         2.93        12.03         6.97        10.06 
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-2874 TCGA-AB-2875 TCGA-AB-2876 
        5.03        20.98         8.98        13.02         6.97        40.08 
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-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
       31.00         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
       22.06         1.94         0.00        17.00        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-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 
       26.04         0.00        29.00        39.98         2.01        12.03 
TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
        0.00         1.02         2.96         7.99        15.02         2.96 
TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 
        4.04         0.00         4.01         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-2959 TCGA-AB-2964 TCGA-AB-2965 
       16.08         6.02        20.02        16.08        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 
       28.08        34.03        15.06        10.03        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 
       20.02         3.02        30.08         1.02        22.98        22.06 
TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 
       22.98        16.01         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 

  SMC1A MUTATED SMC1A WILD-TYPE 
           0.99            0.00 
  SMC1A MUTATED SMC1A WILD-TYPE 
          53.98           94.06 
  SMC1A MUTATED SMC1A WILD-TYPE 
          12.51           12.00 
[1] "1.0 - 54.0 (12.5)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.5"
D21V2, continuous
D21V3, binary
                 cls
clus               0  1
  SMC1A MUTATED    1  5
  SMC1A WILD-TYPE 89 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1A MUTATED      1    5
  SMC1A WILD-TYPE   89   98
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  FEMALE             1              89
  MALE               5              98
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMC1A MUTATED       0                         1     5
  SMC1A WILD-TYPE     2                        14   169
D21V4, multiclass
                           clus
vv                          SMC1A MUTATED SMC1A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                 5             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"
D21V5, binary
                 cls
clus                0   1
  SMC1A MUTATED     0   6
  SMC1A WILD-TYPE   3 181
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1A MUTATED      0    6
  SMC1A WILD-TYPE    3  181
                        clus
vv                       SMC1A MUTATED SMC1A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             181
[1] 2 2
[1] FALSE

Clustering(22) Variable = PTPN11 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED     2   7
  PTPN11 WILD-TYPE  62 108
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              170 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               7              108 
$`PTPN11 MUTATED`
TCGA-AB-2802 TCGA-AB-2839 TCGA-AB-2855 TCGA-AB-2871 TCGA-AB-2884 TCGA-AB-2885 
       12.00        15.98         6.97         5.03        24.03         7.04 
TCGA-AB-2914 TCGA-AB-2963 TCGA-AB-2972 
       26.04        53.98         0.99 

$`PTPN11 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-2812 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2816 
        2.04         1.02        12.03         1.02        26.04         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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
       55.00        17.03        12.00         0.92        46.06         0.00 
TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 
        7.07         4.01         9.99        46.09        19.99        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2857 
       72.99         2.01         7.96         2.93        12.03        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-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 
        5.03        20.98         8.98        13.02         6.97        40.08 
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-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2894 
        5.95        10.98         9.99         0.00        31.00         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-2908 
        1.94         0.00        17.00        52.96        18.97         1.02 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2915 
        0.99         0.00        38.99         9.01        39.98         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-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       20.02        16.08        41.98        11.01        28.08        34.03 
TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       15.06        10.03        26.04        20.02         3.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 
        1.02        22.98        22.06        22.98        16.01         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 

  PTPN11 MUTATED PTPN11 WILD-TYPE 
            0.99             0.00 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           53.98            94.06 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              12               12 
[1] "1.0 - 54.0 (12.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                  cls
clus                0  1
  PTPN11 MUTATED    4  5
  PTPN11 WILD-TYPE 86 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      4    5
  PTPN11 WILD-TYPE   86   98
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  FEMALE              4               86
  MALE                5               98
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN11 MUTATED       0                         1     8
  PTPN11 WILD-TYPE     2                        14   166
D22V4, multiclass
                           clus
vv                          PTPN11 MUTATED PTPN11 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1               14
  WHITE                                  8              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"
D22V5, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     0   9
  PTPN11 WILD-TYPE   3 178
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      0    9
  PTPN11 WILD-TYPE    3  178
                        clus
vv                       PTPN11 MUTATED PTPN11 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              9              178
[1] 2 2
[1] FALSE

Clustering(23) Variable = SUZ12 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  SUZ12 MUTATED     1   2
  SUZ12 WILD-TYPE  63 113
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             176 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2             113 
$`SUZ12 MUTATED`
TCGA-AB-2820 TCGA-AB-2949 TCGA-AB-3009 
        0.00        22.98        18.97 

$`SUZ12 WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
       12.00        26.04        84.07        18.97        31.07         5.95 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2813 TCGA-AB-2814 
       94.06         2.04         1.02        12.03         1.02        26.04 
TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 TCGA-AB-2822 
        8.05         8.98         9.96        82.06        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-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 
        8.98         9.04        21.04        12.00        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
        0.00         7.07         4.01         9.99        46.09        19.99 
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-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
        6.97        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-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 
       13.02         6.97        40.08        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-2894 TCGA-AB-2895 
       10.98         9.99         0.00        31.00         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-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 
       10.06         1.02        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       15.06        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 
       30.08         1.02        22.98        22.06        22.98        16.01 
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-3011 TCGA-AB-3012 
       61.97        62.04 

  SUZ12 MUTATED SUZ12 WILD-TYPE 
              0               0 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
          22.98           94.06 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
          18.97           12.00 
[1] "0.0 - 23.0 (19.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   3
  SUZ12 WILD-TYPE  90 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    3
  SUZ12 WILD-TYPE   90  100
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  FEMALE             0              90
  MALE               3             100
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SUZ12 MUTATED       0                         0     2
  SUZ12 WILD-TYPE     2                        15   172
D23V4, multiclass
[1] "Remove cluster labels:" "SUZ12 MUTATED"         
clus
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2             189 
     TCGA-AB-2802      TCGA-AB-2803      TCGA-AB-2804      TCGA-AB-2805 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2806      TCGA-AB-2807      TCGA-AB-2808      TCGA-AB-2809 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2810      TCGA-AB-2812      TCGA-AB-2813      TCGA-AB-2814 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2816      TCGA-AB-2817      TCGA-AB-2818      TCGA-AB-2819 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2821      TCGA-AB-2822      TCGA-AB-2823      TCGA-AB-2824 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2825      TCGA-AB-2826      TCGA-AB-2827      TCGA-AB-2828 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2829      TCGA-AB-2830      TCGA-AB-2831      TCGA-AB-2832 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2833      TCGA-AB-2834      TCGA-AB-2835      TCGA-AB-2836 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2838      TCGA-AB-2839      TCGA-AB-2840      TCGA-AB-2841 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2842      TCGA-AB-2843      TCGA-AB-2844      TCGA-AB-2845 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2846      TCGA-AB-2847      TCGA-AB-2848      TCGA-AB-2849 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2850      TCGA-AB-2851      TCGA-AB-2853      TCGA-AB-2854 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2855      TCGA-AB-2857      TCGA-AB-2858      TCGA-AB-2859 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2860      TCGA-AB-2861      TCGA-AB-2862      TCGA-AB-2863 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2864      TCGA-AB-2865      TCGA-AB-2866      TCGA-AB-2867 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2868      TCGA-AB-2869      TCGA-AB-2870      TCGA-AB-2871 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2872      TCGA-AB-2873      TCGA-AB-2874      TCGA-AB-2875 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2876      TCGA-AB-2877      TCGA-AB-2878      TCGA-AB-2879 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2880      TCGA-AB-2881      TCGA-AB-2882      TCGA-AB-2883 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2884      TCGA-AB-2885      TCGA-AB-2886      TCGA-AB-2887 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2888      TCGA-AB-2889      TCGA-AB-2890      TCGA-AB-2891 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2892      TCGA-AB-2894      TCGA-AB-2895      TCGA-AB-2896 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2897      TCGA-AB-2898      TCGA-AB-2899      TCGA-AB-2900 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2901      TCGA-AB-2903      TCGA-AB-2904      TCGA-AB-2905 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2906      TCGA-AB-2907      TCGA-AB-2908      TCGA-AB-2909 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2910      TCGA-AB-2911      TCGA-AB-2912      TCGA-AB-2913 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2914      TCGA-AB-2915      TCGA-AB-2916      TCGA-AB-2917 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2918      TCGA-AB-2919      TCGA-AB-2920      TCGA-AB-2921 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2922      TCGA-AB-2923      TCGA-AB-2924      TCGA-AB-2925 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2926      TCGA-AB-2927      TCGA-AB-2928      TCGA-AB-2929 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2930      TCGA-AB-2931      TCGA-AB-2932      TCGA-AB-2933 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2934      TCGA-AB-2935      TCGA-AB-2936      TCGA-AB-2937 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2938      TCGA-AB-2939      TCGA-AB-2940      TCGA-AB-2941 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2942      TCGA-AB-2943      TCGA-AB-2945      TCGA-AB-2946 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2947      TCGA-AB-2948      TCGA-AB-2950      TCGA-AB-2952 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2954      TCGA-AB-2955      TCGA-AB-2956      TCGA-AB-2957 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2959      TCGA-AB-2963      TCGA-AB-2964      TCGA-AB-2965 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2966      TCGA-AB-2967      TCGA-AB-2968      TCGA-AB-2970 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2971      TCGA-AB-2972      TCGA-AB-2973      TCGA-AB-2974 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2975      TCGA-AB-2976      TCGA-AB-2977      TCGA-AB-2978 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2979      TCGA-AB-2980      TCGA-AB-2981      TCGA-AB-2983 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2984      TCGA-AB-2985      TCGA-AB-2986      TCGA-AB-2987 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2988      TCGA-AB-2989      TCGA-AB-2990      TCGA-AB-2991 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2992      TCGA-AB-2993      TCGA-AB-2994      TCGA-AB-2995 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2996      TCGA-AB-2997      TCGA-AB-2998      TCGA-AB-2999 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-3000      TCGA-AB-3001      TCGA-AB-3002      TCGA-AB-3005 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-3006      TCGA-AB-3007      TCGA-AB-3008      TCGA-AB-3011 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-3012 
"SUZ12 WILD-TYPE" 
D23V5, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   2
  SUZ12 WILD-TYPE   3 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    2
  SUZ12 WILD-TYPE    3  185
                        clus
vv                       SUZ12 MUTATED SUZ12 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             185
[1] 2 2
[1] FALSE
