[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/15082450/LAML-TB.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LAML-TB/15166008/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=195, common to both=195
[1] "Reduce the number of clustering variables from 28 to 25."
[1]  25 195
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            53            142 
  FLT3 MUTATED FLT3 WILD-TYPE 
            53            142 
[1] "NPM1 MUTATION ANALYSIS"
[1] 3
  NPM1 MUTATED NPM1 WILD-TYPE 
            52            143 
  NPM1 MUTATED NPM1 WILD-TYPE 
            52            143 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              49              146 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              49              146 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            175 
  IDH2 MUTATED IDH2 WILD-TYPE 
            20            175 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            177 
  IDH1 MUTATED IDH1 WILD-TYPE 
            18            177 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             18             177 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             18             177 
[1] "TET2 MUTATION ANALYSIS"
[1] 3
  TET2 MUTATED TET2 WILD-TYPE 
            17            178 
  TET2 MUTATED TET2 WILD-TYPE 
            17            178 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            180 
  NRAS MUTATED NRAS WILD-TYPE 
            15            180 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           12           183 
  WT1 MUTATED WT1 WILD-TYPE 
           12           183 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             187 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             187 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            15            180 
  TP53 MUTATED TP53 WILD-TYPE 
            15            180 
[1] "CEBPA MUTATION ANALYSIS"
[1] 3
  CEBPA MUTATED CEBPA WILD-TYPE 
             13             182 
  CEBPA MUTATED CEBPA WILD-TYPE 
             13             182 
[1] "PHF6 MUTATION ANALYSIS"
[1] 3
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            189 
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            189 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             8            187 
  KRAS MUTATED KRAS WILD-TYPE 
             8            187 
[1] "SMC3 MUTATION ANALYSIS"
[1] 3
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            188 
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            188 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
            8           187 
  KIT MUTATED KIT WILD-TYPE 
            8           187 
[1] "RAD21 MUTATION ANALYSIS"
[1] 3
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             190 
  RAD21 MUTATED RAD21 WILD-TYPE 
              5             190 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            192 
  EZH2 MUTATED EZH2 WILD-TYPE 
             3            192 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             189 
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             189 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              186 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              186 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             190 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              5             190 
[1] "SUZ12 MUTATION ANALYSIS"
[1] 3
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             192 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             192 
[1] "PHACTR1 MUTATION ANALYSIS"
[1] 3
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               192 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               192 
[1] "SMC1A MUTATION ANALYSIS"
[1] 3
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             189 
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             189 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              3             192 
  KDM6A MUTATED KDM6A WILD-TYPE 
              3             192 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "PRIMARY_SITE_OF_DISEASE"             
 [6] "DCC_UPLOAD_DATE"                     
 [7] "GENDER"                              
 [8] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [9] "DAYS_TO_LAST_KNOWN_ALIVE"            
[10] "KARNOFSKY_PERFORMANCE_SCORE"         
[11] "RACE"                                
[12] "ETHNICITY"                           
[13] "BATCH_NUMBER"                        

Input Data has 13 rows and 195 columns.

[1] "Batch" "13"   
[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:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'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 9:'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 10:'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 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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 195 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 31
  FLT3 WILD-TYPE 47 86
  FLT3 MUTATED FLT3 WILD-TYPE 
            48            133 
  FLT3 MUTATED FLT3 WILD-TYPE 
            31             86 
$`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-2844 TCGA-AB-2851 TCGA-AB-2853 
        8.05        17.03         0.92         4.01         7.96         2.93 
TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2895 
        7.99         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-2988 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2998 TCGA-AB-3006 TCGA-AB-3007 
        0.99        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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2841 TCGA-AB-2842 
       55.00         0.00        12.00        15.98        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-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-2870 TCGA-AB-2872 TCGA-AB-2873 
        5.03         6.05         4.96         5.03        20.98         8.98 
TCGA-AB-2874 TCGA-AB-2876 TCGA-AB-2878 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 
       13.02        40.08        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-2893 TCGA-AB-2894 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
       31.00         6.97         5.95         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2908 
       22.06         1.94         0.00        17.00        52.96         1.02 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 
       38.99         9.01        26.04        29.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2923 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2935 
       12.03         1.02         2.96         4.04         4.01         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2948 
        1.94         7.07         9.99        14.96         0.00        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-2959 TCGA-AB-2964 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2971 
       16.08        41.98        28.08        34.03        15.06        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2982 
        0.99        20.02         1.02        22.98        22.06         4.93 
TCGA-AB-2983 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-2989 TCGA-AB-2990 
       11.01        38.04         8.98         6.05        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2999 TCGA-AB-3000 
       60.03        56.09        50.99        51.98        57.04        41.06 
TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       51.98        47.05        69.04        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

  FLT3 MUTATED FLT3 WILD-TYPE 
             0              0 
  FLT3 MUTATED FLT3 WILD-TYPE 
         59.11          94.06 
  FLT3 MUTATED FLT3 WILD-TYPE 
          8.02          12.92 
[1] "0.0 - 59.1 (8.0)"  "0.0 - 94.1 (12.9)"
[1] "hr=" "1.4"
D1V2, continuous
D1V3, binary
                cls
clus              0  1
  FLT3 MUTATED   27 26
  FLT3 WILD-TYPE 64 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     27   26
  FLT3 WILD-TYPE   64   78
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  FEMALE           27             64
  MALE             26             78
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLT3 MUTATED       2                         5    46
  FLT3 WILD-TYPE     0                        10   130
D1V4, multiclass
                           clus
vv                          FLT3 MUTATED FLT3 WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            5             10
  WHITE                               46            130
[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  53
  FLT3 WILD-TYPE   3 136
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED      0   53
  FLT3 WILD-TYPE    3  136
                        clus
vv                       FLT3 MUTATED FLT3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           53            136
[1] 2 2
[1] FALSE

Clustering(2) Variable = NPM1 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  NPM1 MUTATED   14 37
  NPM1 WILD-TYPE 50 80
  NPM1 MUTATED NPM1 WILD-TYPE 
            51            130 
  NPM1 MUTATED NPM1 WILD-TYPE 
            37             80 
$`NPM1 MUTATED`
TCGA-AB-2802 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2816 TCGA-AB-2818 
       12.00         2.04         1.02        12.03         8.05         9.96 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 
        0.99         6.97        24.03        55.00        17.03         0.00 
TCGA-AB-2839 TCGA-AB-2848 TCGA-AB-2853 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2869 
       15.98        14.96         2.93         9.99         0.00         7.99 
TCGA-AB-2871 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2884 TCGA-AB-2895 TCGA-AB-2896 
        5.03        20.98         8.05        24.03         5.03         7.04 
TCGA-AB-2900 TCGA-AB-2903 TCGA-AB-2913 TCGA-AB-2915 TCGA-AB-2919 TCGA-AB-2924 
        6.05         0.00        39.98         0.00         2.01         2.96 
TCGA-AB-2925 TCGA-AB-2931 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2963 TCGA-AB-2965 
        7.99         0.00         7.99         1.02        53.98        11.01 
TCGA-AB-2967 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2981 
       34.03         0.99        20.02         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-2813 TCGA-AB-2814 TCGA-AB-2817 TCGA-AB-2819 TCGA-AB-2820 TCGA-AB-2821 
        1.02        26.04         8.98        82.06         0.00        27.02 
TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 
       31.99         0.00         8.98        75.09         8.98         9.04 
TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2838 TCGA-AB-2840 
       21.04        12.00        14.99         8.05        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-2854 TCGA-AB-2855 
       19.99        72.99         2.01         7.96        12.03         6.97 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2860 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       10.06        18.97        14.04        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2870 TCGA-AB-2872 
        2.01         5.03         6.05         4.96         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2878 TCGA-AB-2881 
        8.98        13.02         6.97        40.08        12.00        12.92 
TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.00        24.00         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2897 TCGA-AB-2898 
        0.00        31.00         6.97         5.95         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 
       22.06         1.94        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-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2926 TCGA-AB-2927 
       39.98        12.03         0.00         1.02        15.02         2.96 
TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
        4.04         4.01         0.92         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2948 TCGA-AB-2949 
        9.99        14.96         0.00        21.07        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-2964 TCGA-AB-2966 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 
       16.08        41.98        28.08        15.06        10.03        26.04 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
        1.02        22.98        22.06        22.98         4.93        11.01 
TCGA-AB-2985 TCGA-AB-2991 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 
        8.98        60.03        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-3012 
       51.98        27.02        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 
         8.050         12.475 
[1] "0.0 - 62.0 (8.1)"  "0.0 - 94.1 (12.5)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                cls
clus              0  1
  NPM1 MUTATED   29 23
  NPM1 WILD-TYPE 62 81
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPM1 MUTATED     29   23
  NPM1 WILD-TYPE   62   81
        clus
vv       NPM1 MUTATED NPM1 WILD-TYPE
  FEMALE           29             62
  MALE             23             81
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPM1 MUTATED       1                         6    45
  NPM1 WILD-TYPE     1                         9   131
D2V4, multiclass
                           clus
vv                          NPM1 MUTATED NPM1 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            6              9
  WHITE                               45            131
[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
  NPM1 MUTATED     0  52
  NPM1 WILD-TYPE   3 137
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPM1 MUTATED      0   52
  NPM1 WILD-TYPE    3  137
                        clus
vv                       NPM1 MUTATED NPM1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           52            137
[1] 2 2
[1] FALSE

Clustering(3) Variable = DNMT3A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  DNMT3A MUTATED   10 35
  DNMT3A WILD-TYPE 54 82
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              45              136 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              35               82 
$`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-2831 TCGA-AB-2833 TCGA-AB-2839 TCGA-AB-2851 
        6.97         9.04        21.04        14.99        15.98         7.96 
TCGA-AB-2853 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2867 
        2.93         9.99         0.00         1.02        18.97         6.05 
TCGA-AB-2869 TCGA-AB-2873 TCGA-AB-2884 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2898 
        7.99         8.98        24.03         5.03         7.04        12.92 
TCGA-AB-2908 TCGA-AB-2912 TCGA-AB-2916 TCGA-AB-2919 TCGA-AB-2925 TCGA-AB-2931 
        1.02         9.01        29.00         2.01         7.99         0.00 
TCGA-AB-2934 TCGA-AB-2938 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2949 TCGA-AB-2955 
        0.92         9.99         7.99         1.02        22.98        16.08 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2974 TCGA-AB-2981 
       11.01        28.08        34.03        15.06         3.02        16.01 
TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2993 
        6.05         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-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 
        8.98        12.00         8.05        55.00        17.03         0.00 
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-2893 TCGA-AB-2894 TCGA-AB-2897 
        9.99         0.00        31.00         6.97         5.95         7.99 
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-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2913 TCGA-AB-2914 
       18.97         0.99         0.00        38.99        39.98        26.04 
TCGA-AB-2915 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 
        0.00        39.98        12.03         0.00         1.02         2.96 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2936 
       15.02         2.96         4.04         4.01         2.01         1.94 
TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2948 TCGA-AB-2950 
        7.07        14.96         0.00        21.07        19.07        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
        1.02        49.05         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2976 
       41.98        10.03        26.04         0.99        20.02        30.08 
TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
        1.02        22.98        22.06        22.98         4.93        11.01 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
       38.04         8.98         6.97        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 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
               0                0 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           34.03            94.06 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           8.980           12.475 
[1] "0.0 - 34.0 (9.0)"  "0.0 - 94.1 (12.5)"
[1] "hr=" "1.9"
D3V2, continuous
D3V3, binary
                  cls
clus                0  1
  DNMT3A MUTATED   27 22
  DNMT3A WILD-TYPE 64 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     27   22
  DNMT3A WILD-TYPE   64   82
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE             27               64
  MALE               22               82
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED       1                         5    43
  DNMT3A WILD-TYPE     1                        10   133
D3V4, multiclass
                           clus
vv                          DNMT3A MUTATED DNMT3A WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              5               10
  WHITE                                 43              133
[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
  DNMT3A MUTATED     2  47
  DNMT3A WILD-TYPE   1 142
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      2   47
  DNMT3A WILD-TYPE    1  142
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  2                1
  NOT HISPANIC OR LATINO             47              142
[1] 2 2
[1] FALSE

Clustering(4) Variable = IDH2 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED     5  13
  IDH2 WILD-TYPE  59 104
  IDH2 MUTATED IDH2 WILD-TYPE 
            18            163 
  IDH2 MUTATED IDH2 WILD-TYPE 
            13            104 
$`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-2837 TCGA-AB-2838 
       14.99         8.05        55.00        17.03         0.00        12.00 
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-2851 
        9.99        46.09        19.99        14.96        72.99         7.96 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 
        2.93        12.03         6.97        10.06        18.97         9.99 
TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2865 TCGA-AB-2867 
       14.04         0.00        47.01         1.02         2.01         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-2875 TCGA-AB-2876 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 
        6.97        40.08        12.00         8.05        12.92        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       24.00        24.03         7.04         5.95        10.98         9.99 
TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
        7.99        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2935 
       15.02         2.96         4.04         0.00         4.01         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-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
        1.02        22.98        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2967 
        6.02        20.02        53.98        41.98        11.01        34.03 
TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2974 TCGA-AB-2976 
       15.06        10.03        26.04         0.99         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-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 

  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 81 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     10   10
  IDH2 WILD-TYPE   81   94
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE           10             81
  MALE             10             94
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH2 MUTATED       0                         3    17
  IDH2 WILD-TYPE     2                        12   159
D4V4, multiclass
                           clus
vv                          IDH2 MUTATED IDH2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            3             12
  WHITE                               17            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"
D4V5, binary
                cls
clus               0   1
  IDH2 MUTATED     1  19
  IDH2 WILD-TYPE   2 170
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED      1   19
  IDH2 WILD-TYPE    2  170
                        clus
vv                       IDH2 MUTATED IDH2 WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO           19            170
[1] 2 2
[1] FALSE

Clustering(5) Variable = IDH1 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     6  10
  IDH1 WILD-TYPE  58 107
  IDH1 MUTATED IDH1 WILD-TYPE 
            16            165 
  IDH1 MUTATED IDH1 WILD-TYPE 
            10            107 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
        0.00        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-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-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 
       18.97         2.01         5.03         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-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
        7.04         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
       22.06         6.05         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-2920 TCGA-AB-2922 
       26.04         0.00        29.00        39.98        12.03         0.00 
TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        1.02         2.96         7.99         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-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-2947 TCGA-AB-2948 TCGA-AB-2950 
       14.96         0.00        21.07         1.02        19.07        10.06 
TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 
        1.02        49.05        16.08         6.02        20.02        16.08 
TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 
       53.98        41.98        11.01        28.08        34.03        15.06 
TCGA-AB-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-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-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2991 
        8.98         6.97         6.05         0.99        12.00        60.03 
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-3012 
       27.02        18.97        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          11.01 
[1] "1.0 - 62.0 (15.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
                cls
clus              0  1
  IDH1 MUTATED   10  8
  IDH1 WILD-TYPE 81 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     10    8
  IDH1 WILD-TYPE   81   96
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE           10             81
  MALE              8             96
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         2    16
  IDH1 WILD-TYPE     2                        13   160
D5V4, multiclass
                           clus
vv                          IDH1 MUTATED IDH1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            2             13
  WHITE                               16            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"
D5V5, binary
                cls
clus               0   1
  IDH1 MUTATED     0  18
  IDH1 WILD-TYPE   3 171
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0   18
  IDH1 WILD-TYPE    3  171
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           18            171
[1] 2 2
[1] FALSE

Clustering(6) Variable = RUNX1 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED     3  14
  RUNX1 WILD-TYPE  61 103
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             17             164 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             14             103 
$`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-2949 
       22.06         9.01         2.96         4.01         1.94        22.98 
TCGA-AB-2959 TCGA-AB-2970 TCGA-AB-2978 TCGA-AB-2983 TCGA-AB-3009 
       16.08        10.03        22.98        11.01        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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
        0.00        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-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-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 
       72.99         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-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-2892 
       24.03         7.04         5.95        10.98         9.99        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-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-2929 TCGA-AB-2931 
        1.02         2.96         7.99        15.02         4.04         0.00 
TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        0.92         2.01         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2952 
       21.07         7.99         1.02        19.07        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2963 TCGA-AB-2964 
       49.05        16.08         6.02        20.02        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2971 TCGA-AB-2972 
       11.01        28.08        34.03        15.06        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2980 
       20.02         3.02        30.08         1.02        22.06        22.98 
TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
       16.01         4.93        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 
          10.03           12.00 
[1] "0.0 - 27.0 (10.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.7"
D6V2, continuous
D6V3, binary
                 cls
clus               0  1
  RUNX1 MUTATED    7 11
  RUNX1 WILD-TYPE 84 93
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      7   11
  RUNX1 WILD-TYPE   84   93
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  FEMALE             7              84
  MALE              11              93
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RUNX1 MUTATED       0                         1    16
  RUNX1 WILD-TYPE     2                        14   160
D6V4, multiclass
                           clus
vv                          RUNX1 MUTATED RUNX1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                16             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"
D6V5, binary
                 cls
clus                0   1
  RUNX1 MUTATED     0  17
  RUNX1 WILD-TYPE   3 172
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED      0   17
  RUNX1 WILD-TYPE    3  172
                        clus
vv                       RUNX1 MUTATED RUNX1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            17             172
[1] 2 2
[1] FALSE

Clustering(7) Variable = TET2 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  TET2 MUTATED     6  10
  TET2 WILD-TYPE  58 107
  TET2 MUTATED TET2 WILD-TYPE 
            16            165 
  TET2 MUTATED TET2 WILD-TYPE 
            10            107 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 
        0.00         7.07         4.01        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-2864 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
        1.02        18.97         5.03         6.05         4.96         7.99 
TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 
        5.03         5.03        20.98        13.02         6.97        20.98 
TCGA-AB-2878 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 
       12.00        12.92        12.00        24.00        24.03         7.04 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
        5.95         5.03         7.04         7.99        12.92        22.06 
TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
        6.05         1.94         0.00        17.00        52.96        18.97 
TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 
        0.99         0.00        38.99         9.01        39.98        26.04 
TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 
        0.00        29.00        39.98         2.01        12.03         0.00 
TCGA-AB-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-2938 TCGA-AB-2939 
        4.01         0.92         2.01         1.94         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-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2970 
       16.08        53.98        28.08        34.03        15.06        10.03 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 
        0.99        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-2998 TCGA-AB-2999 
       56.09        25.02        59.11        50.99         1.02        57.04 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3007 TCGA-AB-3008 
       41.06        51.98        47.05        69.04        51.98        27.02 
TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       18.97        61.97        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"
D7V2, continuous
D7V3, binary
                cls
clus              0  1
  TET2 MUTATED   10  7
  TET2 WILD-TYPE 81 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET2 MUTATED     10    7
  TET2 WILD-TYPE   81   97
        clus
vv       TET2 MUTATED TET2 WILD-TYPE
  FEMALE           10             81
  MALE              7             97
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TET2 MUTATED       0                         1    16
  TET2 WILD-TYPE     2                        14   160
D7V4, multiclass
                           clus
vv                          TET2 MUTATED TET2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1             14
  WHITE                               16            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"
D7V5, binary
                cls
clus               0   1
  TET2 MUTATED     0  17
  TET2 WILD-TYPE   3 172
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET2 MUTATED      0   17
  TET2 WILD-TYPE    3  172
                        clus
vv                       TET2 MUTATED TET2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           17            172
[1] 2 2
[1] FALSE

Clustering(8) Variable = NRAS MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     5   8
  NRAS WILD-TYPE  59 109
  NRAS MUTATED NRAS WILD-TYPE 
            13            168 
  NRAS MUTATED NRAS WILD-TYPE 
             8            109 
$`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-2837 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 
       17.03         0.00         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-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-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-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       22.06         6.05         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 
       39.98        26.04         0.00        29.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 
       12.03         0.00         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-2954 TCGA-AB-2955 
        1.02        19.07        22.98        10.06        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-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 
       28.08        10.03        26.04         0.99        20.02         3.02 
TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 
       30.08         1.02        22.06        22.98        16.01         4.93 
TCGA-AB-2983 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 
       11.01         6.97         6.05         0.99        12.00        15.02 
TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2996 
       60.03        56.09        25.02        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  NRAS MUTATED NRAS WILD-TYPE 
          1.02           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
         94.06          84.07 
  NRAS MUTATED NRAS WILD-TYPE 
        15.060         11.505 
[1] "1.0 - 94.1 (15.1)" "0.0 - 84.1 (11.5)"
[1] "hr=" "1.2"
D8V2, continuous
D8V3, binary
                cls
clus              0  1
  NRAS MUTATED    7  8
  NRAS WILD-TYPE 84 96
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      7    8
  NRAS WILD-TYPE   84   96
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            7             84
  MALE              8             96
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED       0                         0    15
  NRAS WILD-TYPE     2                        15   161
D8V4, multiclass
                           clus
vv                          NRAS MUTATED NRAS WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                               15            161
[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
  NRAS MUTATED     0  15
  NRAS WILD-TYPE   3 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0   15
  NRAS WILD-TYPE    3  174
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           15            174
[1] 2 2
[1] FALSE

Clustering(9) Variable = WT1 MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  WT1 MUTATED     4   7
  WT1 WILD-TYPE  60 110
  WT1 MUTATED WT1 WILD-TYPE 
           11           170 
  WT1 MUTATED WT1 WILD-TYPE 
            7           110 
$`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-2837 TCGA-AB-2838 TCGA-AB-2840 
        8.05        55.00        17.03         0.00        12.00         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2845 TCGA-AB-2847 TCGA-AB-2848 
       46.06         0.00         7.07         9.99        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-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-2875 
        7.99         5.03         5.03        20.98         8.98         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-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       17.00        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2920 
        9.01        26.04         0.00        29.00        39.98        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-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-2971 TCGA-AB-2972 
       11.01        28.08        34.03        15.06        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 
       20.02         3.02         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-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 
        6.05         0.99        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 

  WT1 MUTATED WT1 WILD-TYPE 
         2.01          0.00 
  WT1 MUTATED WT1 WILD-TYPE 
        52.96         94.06 
  WT1 MUTATED WT1 WILD-TYPE 
        15.98         11.01 
[1] "2.0 - 53.0 (16.0)" "0.0 - 94.1 (11.0)"
[1] "hr=" "1.3"
D9V2, continuous
D9V3, binary
               cls
clus             0  1
  WT1 MUTATED    5  7
  WT1 WILD-TYPE 86 97
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      5    7
  WT1 WILD-TYPE   86   97
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  FEMALE           5            86
  MALE             7            97
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WT1 MUTATED       0                         0    11
  WT1 WILD-TYPE     2                        15   165
D9V4, multiclass
                           clus
vv                          WT1 MUTATED WT1 WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0            15
  WHITE                              11           165
[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
  WT1 MUTATED     1  10
  WT1 WILD-TYPE   2 179
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      1   10
  WT1 WILD-TYPE    2  179
                        clus
vv                       WT1 MUTATED WT1 WILD-TYPE
  HISPANIC OR LATINO               1             2
  NOT HISPANIC OR LATINO          10           179
[1] 2 2
[1] FALSE

Clustering(10) Variable = U2AF1 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  U2AF1 MUTATED     1   7
  U2AF1 WILD-TYPE  63 110
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              8             173 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              7             110 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 
       72.99         2.01         7.96         2.93        12.03         6.97 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2862 TCGA-AB-2863 
       10.06        18.97         9.99        14.04        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-2883 
       40.08        20.98        12.00         8.05        12.92        24.00 
TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 
       24.03         7.04         5.95        10.98         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-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-2935 
        2.96         4.04         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        1.94         7.07         9.99        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        7.99         1.02        19.07        22.98        10.06         1.02 
TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       49.05        16.08         6.02        20.02        16.08        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2970 TCGA-AB-2971 
       41.98        11.01        28.08        34.03        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-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-2998 
       60.03        56.09        25.02        59.11        50.99         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 

  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"
D10V2, continuous
D10V3, binary
                 cls
clus               0  1
  U2AF1 MUTATED    1  7
  U2AF1 WILD-TYPE 90 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      1    7
  U2AF1 WILD-TYPE   90   97
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  FEMALE             1              90
  MALE               7              97
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  U2AF1 MUTATED       0                         0     8
  U2AF1 WILD-TYPE     2                        15   168
D10V4, multiclass
                           clus
vv                          U2AF1 MUTATED U2AF1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0              15
  WHITE                                 8             168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                 cls
clus                0   1
  U2AF1 MUTATED     0   7
  U2AF1 WILD-TYPE   3 182
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      0    7
  U2AF1 WILD-TYPE    3  182
                        clus
vv                       U2AF1 MUTATED U2AF1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             7             182
[1] 2 2
[1] FALSE

Clustering(11) Variable = TP53 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     0  14
  TP53 WILD-TYPE  64 103
  TP53 MUTATED TP53 WILD-TYPE 
            14            167 
  TP53 MUTATED TP53 WILD-TYPE 
            14            103 
$`TP53 MUTATED`
TCGA-AB-2813 TCGA-AB-2820 TCGA-AB-2829 TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2868 
        1.02         0.00         8.98        10.06        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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 
        0.00        12.00        15.98         0.92        46.06         0.00 
TCGA-AB-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-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 
       18.97         9.99         0.00        47.01         1.02        18.97 
TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 
        2.01         5.03         6.05         7.99         5.03         5.03 
TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 
       20.98         8.98        13.02         6.97        40.08        20.98 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2886 
        8.05        12.92        12.00        24.00        24.03         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 
        1.94         0.00        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-2923 TCGA-AB-2924 
       39.98         2.01        12.03         0.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        7.99        15.02         2.96         4.04         0.00         4.01 
TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2942 TCGA-AB-2945 
        0.92         1.94         7.07        14.96        21.07         7.99 
TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 
        1.02        19.07        22.98        10.06        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-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 

  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=" "3.5"
D11V2, continuous
D11V3, binary
                cls
clus              0  1
  TP53 MUTATED    4 11
  TP53 WILD-TYPE 87 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   11
  TP53 WILD-TYPE   87   93
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            4             87
  MALE             11             93
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         1    14
  TP53 WILD-TYPE     2                        14   162
D11V4, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1             14
  WHITE                               14            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
  TP53 MUTATED     0  15
  TP53 WILD-TYPE   3 174
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   15
  TP53 WILD-TYPE    3  174
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           15            174
[1] 2 2
[1] FALSE

Clustering(12) Variable = CEBPA MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  CEBPA MUTATED     4   7
  CEBPA WILD-TYPE  60 110
  CEBPA MUTATED CEBPA WILD-TYPE 
             11             170 
  CEBPA MUTATED CEBPA WILD-TYPE 
              7             110 
$`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-2837 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        12.00         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 
        0.00         7.07         4.01        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-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-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       12.92        22.06         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 
       39.98        26.04         0.00        29.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 
       12.03         0.00         1.02         2.96         7.99        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
        2.96         4.04         0.00         4.01         0.92         2.01 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 
        1.94         7.07         9.99        14.96         0.00        21.07 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2954 
        7.99         1.02        19.07        22.98        10.06        49.05 
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-2980 
       20.02         3.02        30.08         1.02        22.98        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-2996 TCGA-AB-2998 TCGA-AB-2999 
       25.02        59.11        50.99        51.98         1.02        57.04 
TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3009 
       51.98        47.05        69.04        15.95        51.98        18.97 
TCGA-AB-3011 TCGA-AB-3012 
       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 
         15.980          11.505 
[1] "1.0 - 94.1 (16.0)" "0.0 - 84.1 (11.5)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                 cls
clus               0  1
  CEBPA MUTATED    5  8
  CEBPA WILD-TYPE 86 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED      5    8
  CEBPA WILD-TYPE   86   96
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  FEMALE             5              86
  MALE               8              96
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEBPA MUTATED       0                         1    12
  CEBPA WILD-TYPE     2                        14   164
D12V4, multiclass
                           clus
vv                          CEBPA MUTATED CEBPA WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                12             164
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                 cls
clus                0   1
  CEBPA MUTATED     0  13
  CEBPA WILD-TYPE   3 176
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED      0   13
  CEBPA WILD-TYPE    3  176
                        clus
vv                       CEBPA MUTATED CEBPA WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO            13             176
[1] 2 2
[1] FALSE

Clustering(13) Variable = PHF6 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  PHF6 MUTATED     1   5
  PHF6 WILD-TYPE  63 112
  PHF6 MUTATED PHF6 WILD-TYPE 
             6            175 
  PHF6 MUTATED PHF6 WILD-TYPE 
             5            112 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 TCGA-AB-2853 
       19.99        14.96        72.99         2.01         7.96         2.93 
TCGA-AB-2854 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 
       12.03        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-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 
        1.94         0.00        17.00        52.96        18.97         1.02 
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-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-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       20.02        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-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-3011 
       47.05        69.04        15.95        51.98        27.02        61.97 
TCGA-AB-3012 
       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"  
D13V2, continuous
D13V3, binary
                cls
clus              0  1
  PHF6 MUTATED    0  6
  PHF6 WILD-TYPE 91 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF6 MUTATED      0    6
  PHF6 WILD-TYPE   91   98
        clus
vv       PHF6 MUTATED PHF6 WILD-TYPE
  FEMALE            0             91
  MALE              6             98
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF6 MUTATED       0                         0     5
  PHF6 WILD-TYPE     2                        15   171
D13V4, multiclass
                           clus
vv                          PHF6 MUTATED PHF6 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                5            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"
D13V5, binary
                cls
clus               0   1
  PHF6 MUTATED     0   5
  PHF6 WILD-TYPE   3 184
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF6 MUTATED      0    5
  PHF6 WILD-TYPE    3  184
                        clus
vv                       PHF6 MUTATED PHF6 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            5            184
[1] 2 2
[1] FALSE

Clustering(14) Variable = KRAS MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     1   7
  KRAS WILD-TYPE  63 110
  KRAS MUTATED KRAS WILD-TYPE 
             8            173 
  KRAS MUTATED KRAS WILD-TYPE 
             7            110 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 TCGA-AB-2853 
       19.99        14.96        72.99         2.01         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-2862 TCGA-AB-2863 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 
       47.01         1.02         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-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 
        7.99        12.92        22.06         6.05         1.94         0.00 
TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 
       17.00        52.96        18.97         1.02         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
       38.99         9.01        39.98        26.04         0.00        29.00 
TCGA-AB-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-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
       15.02         2.96         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-2967 TCGA-AB-2968 TCGA-AB-2970 TCGA-AB-2971 
       41.98        11.01        34.03        15.06        10.03        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2978 
        0.99        20.02         3.02        30.08         1.02        22.98 
TCGA-AB-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-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2991 
        8.98         6.97         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 

  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"
D14V2, continuous
D14V3, binary
                cls
clus               0   1
  KRAS MUTATED     6   2
  KRAS WILD-TYPE  85 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6    2
  KRAS WILD-TYPE   85  102
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            6             85
  MALE              2            102
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       0                         0     8
  KRAS WILD-TYPE     2                        15   168
D14V4, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                8            168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                cls
clus               0   1
  KRAS MUTATED     1   7
  KRAS WILD-TYPE   2 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      1    7
  KRAS WILD-TYPE    2  182
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                1              2
  NOT HISPANIC OR LATINO            7            182
[1] 2 2
[1] FALSE

Clustering(15) Variable = SMC3 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2              0   1
  SMC3 MUTATED     1   6
  SMC3 WILD-TYPE  63 111
  SMC3 MUTATED SMC3 WILD-TYPE 
             7            174 
  SMC3 MUTATED SMC3 WILD-TYPE 
             6            111 
$`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-2837 TCGA-AB-2838 TCGA-AB-2840 
        8.05        55.00        17.03         0.00        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-2848 TCGA-AB-2849 TCGA-AB-2850 TCGA-AB-2854 TCGA-AB-2855 
       19.99        14.96        72.99         2.01        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-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-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 
        0.00        17.00        52.96        18.97         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-2952 
       21.07         7.99         1.02        19.07        22.98         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-2994 TCGA-AB-2995 TCGA-AB-2996 
       15.02        60.03        56.09        59.11        50.99        51.98 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3005 
        1.02        57.04        41.06        51.98        47.05        69.04 
TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 TCGA-AB-3012 
       15.95        51.98        27.02        18.97        61.97        62.04 

  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"
D15V2, continuous
D15V3, binary
                cls
clus               0   1
  SMC3 MUTATED     4   3
  SMC3 WILD-TYPE  87 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      4    3
  SMC3 WILD-TYPE   87  101
        clus
vv       SMC3 MUTATED SMC3 WILD-TYPE
  FEMALE            4             87
  MALE              3            101
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMC3 MUTATED       0                         0     7
  SMC3 WILD-TYPE     2                        15   169
D15V4, multiclass
                           clus
vv                          SMC3 MUTATED SMC3 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                7            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"
D15V5, binary
                cls
clus               0   1
  SMC3 MUTATED     0   7
  SMC3 WILD-TYPE   3 182
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC3 MUTATED      0    7
  SMC3 WILD-TYPE    3  182
                        clus
vv                       SMC3 MUTATED SMC3 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            7            182
[1] 2 2
[1] FALSE

Clustering(16) Variable = KIT MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  KIT MUTATED     4   4
  KIT WILD-TYPE  60 113
  KIT MUTATED KIT WILD-TYPE 
            8           173 
  KIT MUTATED KIT WILD-TYPE 
            4           113 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2847 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        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-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-2882 
        6.97        40.08        20.98        12.00         8.05        12.00 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2889 TCGA-AB-2890 
       24.00        24.03         7.04         5.95         9.99         0.00 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 
       31.00         6.97         5.95         5.03         7.04         7.99 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
       12.92        22.06         6.05         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2938 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2947 
        2.01         1.94         9.99         0.00        21.07         1.02 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
       19.07        22.98        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
        6.02        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-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 

  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=" "1.5"
D16V2, continuous
D16V3, binary
               cls
clus              0   1
  KIT MUTATED     5   3
  KIT WILD-TYPE  86 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      5    3
  KIT WILD-TYPE   86  101
        clus
vv       KIT MUTATED KIT WILD-TYPE
  FEMALE           5            86
  MALE             3           101
[1] 2 2
[1] FALSE
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIT MUTATED       0                         0     8
  KIT WILD-TYPE     2                        15   168
D16V4, multiclass
                           clus
vv                          KIT MUTATED KIT WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0            15
  WHITE                               8           168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
               cls
clus              0   1
  KIT MUTATED     0   8
  KIT WILD-TYPE   3 181
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED      0    8
  KIT WILD-TYPE    3  181
                        clus
vv                       KIT MUTATED KIT WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           8           181
[1] 2 2
[1] FALSE

Clustering(17) Variable = RAD21 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  RAD21 MUTATED     2   2
  RAD21 WILD-TYPE  62 115
  RAD21 MUTATED RAD21 WILD-TYPE 
              4             177 
  RAD21 MUTATED RAD21 WILD-TYPE 
              2             115 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 TCGA-AB-2853 
       19.99        14.96        72.99         2.01         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-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        6.05         4.96         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 
        8.98        13.02         6.97        40.08        20.98        12.00 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 
        8.05        12.92        12.00        24.00        24.03         7.04 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-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-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-2968 TCGA-AB-2970 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       28.08        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-2987 
       16.01         4.93        11.01        38.04         8.98         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 

  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  89 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED      2    3
  RAD21 WILD-TYPE   89  101
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  FEMALE             2              89
  MALE               3             101
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAD21 MUTATED       1                         1     3
  RAD21 WILD-TYPE     1                        14   173
D17V4, multiclass
                           clus
vv                          RAD21 MUTATED RAD21 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                 3             173
[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   3 184
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED      0    5
  RAD21 WILD-TYPE    3  184
                        clus
vv                       RAD21 MUTATED RAD21 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5             184
[1] 2 2
[1] FALSE

Clustering(18) Variable = EZH2 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED     0   2
  EZH2 WILD-TYPE  64 115
  EZH2 MUTATED EZH2 WILD-TYPE 
             2            179 
  EZH2 MUTATED EZH2 WILD-TYPE 
             2            115 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 TCGA-AB-2853 
       19.99        14.96        72.99         2.01         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-2864 TCGA-AB-2866 TCGA-AB-2867 
        0.00        47.01         1.02        18.97         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-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-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-2952 TCGA-AB-2954 TCGA-AB-2955 
       19.07        22.98        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
        6.02        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-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 

  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  90 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      1    2
  EZH2 WILD-TYPE   90  102
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  FEMALE            1             90
  MALE              2            102
[1] 2 2
[1] FALSE
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EZH2 MUTATED       0                         0     3
  EZH2 WILD-TYPE     2                        15   173
D18V4, multiclass
                           clus
vv                          EZH2 MUTATED EZH2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0             15
  WHITE                                3            173
[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   3 186
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      0    3
  EZH2 WILD-TYPE    3  186
                        clus
vv                       EZH2 MUTATED EZH2 WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO            3            186
[1] 2 2
[1] FALSE

Clustering(19) Variable = STAG2 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     4   2
  STAG2 WILD-TYPE  60 115
  STAG2 MUTATED STAG2 WILD-TYPE 
              6             175 
  STAG2 MUTATED STAG2 WILD-TYPE 
              2             115 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2872 TCGA-AB-2873 
        6.05         4.96         7.99         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-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-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-2915 
        0.99         0.00        38.99         9.01        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 
       22.98        10.06         1.02        49.05        16.08         6.02 
TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 
       20.02        16.08        53.98        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-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 
        1.02        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 

  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"  
D19V2, continuous
D19V3, binary
                 cls
clus                0   1
  STAG2 MUTATED     4   2
  STAG2 WILD-TYPE  87 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      4    2
  STAG2 WILD-TYPE   87  102
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             4              87
  MALE               2             102
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED       0                         2     4
  STAG2 WILD-TYPE     2                        13   172
D19V4, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2              13
  WHITE                                 4             172
[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
  STAG2 MUTATED     0   6
  STAG2 WILD-TYPE   3 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    6
  STAG2 WILD-TYPE    3  183
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             183
[1] 2 2
[1] FALSE

Clustering(20) Variable = PTPN11 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED     2   7
  PTPN11 WILD-TYPE  62 110
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               9              172 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
               7              110 
$`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-2837 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 
       55.00        17.03         0.00        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-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-2872 TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 
        7.99         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-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 
       24.00         5.95        10.98         9.99         0.00        31.00 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
        6.97         5.95         5.03         7.04         7.99        12.92 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
       22.06         6.05         1.94         0.00        17.00        52.96 
TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 
       18.97         1.02         0.99         0.00        38.99         9.01 
TCGA-AB-2913 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 
       39.98         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-2973 
       28.08        34.03        15.06        10.03        26.04        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-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 

  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=" "1.2"
D20V2, continuous
D20V3, binary
                  cls
clus                0  1
  PTPN11 MUTATED    4  5
  PTPN11 WILD-TYPE 87 99
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      4    5
  PTPN11 WILD-TYPE   87   99
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  FEMALE              4               87
  MALE                5               99
[1] 2 2
[1] FALSE
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN11 MUTATED       0                         1     8
  PTPN11 WILD-TYPE     2                        14   168
D20V4, multiclass
                           clus
vv                          PTPN11 MUTATED PTPN11 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1               14
  WHITE                                  8              168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                  cls
clus                 0   1
  PTPN11 MUTATED     0   9
  PTPN11 WILD-TYPE   3 180
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED      0    9
  PTPN11 WILD-TYPE    3  180
                        clus
vv                       PTPN11 MUTATED PTPN11 WILD-TYPE
  HISPANIC OR LATINO                  0                3
  NOT HISPANIC OR LATINO              9              180
[1] 2 2
[1] FALSE

Clustering(21) Variable = ASXL1 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED     0   4
  ASXL1 WILD-TYPE  64 113
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              4             177 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
              4             113 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-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-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
       47.01         1.02         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-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 
        2.96         7.99        15.02         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 

  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"
D21V2, continuous
D21V3, binary
                 cls
clus                0   1
  ASXL1 MUTATED     3   2
  ASXL1 WILD-TYPE  88 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      3    2
  ASXL1 WILD-TYPE   88  102
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE             3              88
  MALE               2             102
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED       0                         0     5
  ASXL1 WILD-TYPE     2                        15   171
D21V4, multiclass
                           clus
vv                          ASXL1 MUTATED ASXL1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0              15
  WHITE                                 5             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"
D21V5, binary
                 cls
clus                0   1
  ASXL1 MUTATED     1   4
  ASXL1 WILD-TYPE   2 185
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED      1    4
  ASXL1 WILD-TYPE    2  185
                        clus
vv                       ASXL1 MUTATED ASXL1 WILD-TYPE
  HISPANIC OR LATINO                 1               2
  NOT HISPANIC OR LATINO             4             185
[1] 2 2
[1] FALSE

Clustering(22) Variable = SUZ12 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  SUZ12 MUTATED     1   2
  SUZ12 WILD-TYPE  63 115
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3             178 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2             115 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 TCGA-AB-2853 
       19.99        14.96        72.99         2.01         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-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
        6.05         4.96         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 
        8.98        13.02         6.97        40.08        20.98        12.00 
TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 
        8.05        12.92        12.00        24.00        24.03         7.04 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
        5.95         5.03         7.04         7.99        12.92        22.06 
TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 
        6.05         1.94         0.00        17.00        52.96        18.97 
TCGA-AB-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-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
        1.02        19.07        10.06         1.02        49.05        16.08 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
        6.02        20.02        16.08        53.98        41.98        11.01 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-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-3011 TCGA-AB-3012 
       51.98        27.02        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"
D22V2, continuous
D22V3, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   3
  SUZ12 WILD-TYPE  91 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    3
  SUZ12 WILD-TYPE   91  101
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  FEMALE             0              91
  MALE               3             101
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SUZ12 MUTATED       0                         0     2
  SUZ12 WILD-TYPE     2                        15   174
D22V4, multiclass
[1] "Remove cluster labels:" "SUZ12 MUTATED"         
clus
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2             191 
     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-2837      TCGA-AB-2838      TCGA-AB-2839      TCGA-AB-2840 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2841      TCGA-AB-2842      TCGA-AB-2843      TCGA-AB-2844 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2845      TCGA-AB-2846      TCGA-AB-2847      TCGA-AB-2848 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2849      TCGA-AB-2850      TCGA-AB-2851      TCGA-AB-2853 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2854      TCGA-AB-2855      TCGA-AB-2857      TCGA-AB-2858 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2859      TCGA-AB-2860      TCGA-AB-2861      TCGA-AB-2862 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2863      TCGA-AB-2864      TCGA-AB-2865      TCGA-AB-2866 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2867      TCGA-AB-2868      TCGA-AB-2869      TCGA-AB-2870 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2871      TCGA-AB-2872      TCGA-AB-2873      TCGA-AB-2874 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2875      TCGA-AB-2876      TCGA-AB-2877      TCGA-AB-2878 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2879      TCGA-AB-2880      TCGA-AB-2881      TCGA-AB-2882 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2883      TCGA-AB-2884      TCGA-AB-2885      TCGA-AB-2886 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2887      TCGA-AB-2888      TCGA-AB-2889      TCGA-AB-2890 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2891      TCGA-AB-2892      TCGA-AB-2893      TCGA-AB-2894 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2895      TCGA-AB-2896      TCGA-AB-2897      TCGA-AB-2898 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2899      TCGA-AB-2900      TCGA-AB-2901      TCGA-AB-2903 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2904      TCGA-AB-2905      TCGA-AB-2906      TCGA-AB-2907 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2908      TCGA-AB-2909      TCGA-AB-2910      TCGA-AB-2911 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2912      TCGA-AB-2913      TCGA-AB-2914      TCGA-AB-2915 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2916      TCGA-AB-2917      TCGA-AB-2918      TCGA-AB-2919 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2920      TCGA-AB-2921      TCGA-AB-2922      TCGA-AB-2923 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2924      TCGA-AB-2925      TCGA-AB-2926      TCGA-AB-2927 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2928      TCGA-AB-2929      TCGA-AB-2930      TCGA-AB-2931 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2932      TCGA-AB-2933      TCGA-AB-2934      TCGA-AB-2935 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2936      TCGA-AB-2937      TCGA-AB-2938      TCGA-AB-2939 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2940      TCGA-AB-2941      TCGA-AB-2942      TCGA-AB-2943 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2945      TCGA-AB-2946      TCGA-AB-2947      TCGA-AB-2948 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2950      TCGA-AB-2952      TCGA-AB-2954      TCGA-AB-2955 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2956      TCGA-AB-2957      TCGA-AB-2959      TCGA-AB-2963 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2964      TCGA-AB-2965      TCGA-AB-2966      TCGA-AB-2967 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2968      TCGA-AB-2970      TCGA-AB-2971      TCGA-AB-2972 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2973      TCGA-AB-2974      TCGA-AB-2975      TCGA-AB-2976 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2977      TCGA-AB-2978      TCGA-AB-2979      TCGA-AB-2980 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2981      TCGA-AB-2983      TCGA-AB-2984      TCGA-AB-2985 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2986      TCGA-AB-2987      TCGA-AB-2988      TCGA-AB-2989 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2990      TCGA-AB-2991      TCGA-AB-2992      TCGA-AB-2993 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2994      TCGA-AB-2995      TCGA-AB-2996      TCGA-AB-2997 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-2998      TCGA-AB-2999      TCGA-AB-3000      TCGA-AB-3001 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-3002      TCGA-AB-3005      TCGA-AB-3006      TCGA-AB-3007 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-AB-3008      TCGA-AB-3011      TCGA-AB-3012 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
D22V5, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   2
  SUZ12 WILD-TYPE   3 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    2
  SUZ12 WILD-TYPE    3  187
                        clus
vv                       SUZ12 MUTATED SUZ12 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2             187
[1] 2 2
[1] FALSE

Clustering(23) Variable = PHACTR1 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                 0   1
  PHACTR1 MUTATED     2   1
  PHACTR1 WILD-TYPE  62 116
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                3               178 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
                1               116 
$`PHACTR1 MUTATED`
TCGA-AB-2868 TCGA-AB-2876 TCGA-AB-2916 
        4.96        40.08        29.00 

$`PHACTR1 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-2837 TCGA-AB-2838 TCGA-AB-2839 
        8.05        55.00        17.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 
       46.09        19.99        14.96        72.99         2.01         7.96 
TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 
        2.93        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-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-2877 TCGA-AB-2878 TCGA-AB-2879 
        8.98        13.02         6.97        20.98        12.00         8.05 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 
       12.92        12.00        24.00        24.03         7.04         5.95 
TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 
       10.98         9.99         0.00        31.00         6.97         5.95 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 
        5.03         7.04         7.99        12.92        22.06         6.05 
TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-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-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
        0.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 
       22.98        10.06         1.02        49.05        16.08         6.02 
TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2966 
       20.02        16.08        53.98        41.98        11.01        28.08 
TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-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-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 

  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
             4.96              0.00 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
            40.08             94.06 
  PHACTR1 MUTATED PHACTR1 WILD-TYPE 
               29                12 
[1] "5.0 - 40.1 (29.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "2.6"
D23V2, continuous
D23V3, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     2   1
  PHACTR1 WILD-TYPE  89 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      2    1
  PHACTR1 WILD-TYPE   89  103
        clus
vv       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  FEMALE               2                89
  MALE                 1               103
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHACTR1 MUTATED       0                         0     3
  PHACTR1 WILD-TYPE     2                        15   173
D23V4, multiclass
                           clus
vv                          PHACTR1 MUTATED PHACTR1 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                15
  WHITE                                   3               173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                   cls
clus                  0   1
  PHACTR1 MUTATED     1   2
  PHACTR1 WILD-TYPE   2 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PHACTR1 MUTATED      1    2
  PHACTR1 WILD-TYPE    2  187
                        clus
vv                       PHACTR1 MUTATED PHACTR1 WILD-TYPE
  HISPANIC OR LATINO                   1                 2
  NOT HISPANIC OR LATINO               2               187
[1] 2 2
[1] FALSE

Clustering(24) Variable = SMC1A MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  SMC1A MUTATED     0   6
  SMC1A WILD-TYPE  64 111
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             175 
  SMC1A MUTATED SMC1A WILD-TYPE 
              6             111 
$`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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
       17.03         0.00        12.00        15.98         0.92        46.06 
TCGA-AB-2842 TCGA-AB-2843 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 
        0.00         7.07         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-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 
       10.06         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-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
        0.00        31.00         6.97         5.95         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 
        7.99        12.92        22.06         1.94         0.00        17.00 
TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
       52.96        18.97         1.02         0.99         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
        9.01        39.98        26.04         0.00        29.00        39.98 
TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        2.01        12.03         0.00         1.02         2.96         7.99 
TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
       15.02         2.96         4.04         0.00         4.01         0.92 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 
        2.01         1.94         7.07         9.99        14.96         0.00 
TCGA-AB-2942 TCGA-AB-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-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 

  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"
D24V2, continuous
D24V3, binary
                 cls
clus               0  1
  SMC1A MUTATED    1  5
  SMC1A WILD-TYPE 90 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1A MUTATED      1    5
  SMC1A WILD-TYPE   90   99
        clus
vv       SMC1A MUTATED SMC1A WILD-TYPE
  FEMALE             1              90
  MALE               5              99
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMC1A MUTATED       0                         1     5
  SMC1A WILD-TYPE     2                        14   171
D24V4, multiclass
                           clus
vv                          SMC1A MUTATED SMC1A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1              14
  WHITE                                 5             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"
D24V5, binary
                 cls
clus                0   1
  SMC1A MUTATED     0   6
  SMC1A WILD-TYPE   3 183
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1A MUTATED      0    6
  SMC1A WILD-TYPE    3  183
                        clus
vv                       SMC1A MUTATED SMC1A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             6             183
[1] 2 2
[1] FALSE

Clustering(25) Variable = KDM6A MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     1   2
  KDM6A WILD-TYPE  63 115
  KDM6A MUTATED KDM6A WILD-TYPE 
              3             178 
  KDM6A MUTATED KDM6A WILD-TYPE 
              2             115 
$`KDM6A MUTATED`
TCGA-AB-2806 TCGA-AB-2867 TCGA-AB-2883 
       31.07         6.05        24.00 

$`KDM6A WILD-TYPE`
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2808 
       12.00        26.04        84.07        18.97         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-2837 TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 
       55.00        17.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-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-2850 TCGA-AB-2851 TCGA-AB-2853 
       19.99        14.96        72.99         2.01         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-2864 TCGA-AB-2865 TCGA-AB-2866 
        0.00        47.01         1.02        18.97         2.01         5.03 
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-2884 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2888 
       12.92        12.00        24.03         7.04         5.95        10.98 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        9.99         0.00        31.00         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 
        7.04         7.99        12.92        22.06         6.05         1.94 
TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2908 TCGA-AB-2909 
        0.00        17.00        52.96        18.97         1.02         0.99 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 
        0.00        38.99         9.01        39.98        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2923 
       29.00        39.98         2.01        12.03         0.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2931 
        2.96         7.99        15.02         2.96         4.04         0.00 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        4.01         0.92         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
       14.96         0.00        21.07         7.99         1.02        19.07 
TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-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-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-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 

  KDM6A MUTATED KDM6A WILD-TYPE 
           6.05            0.00 
  KDM6A MUTATED KDM6A WILD-TYPE 
          31.07           94.06 
  KDM6A MUTATED KDM6A WILD-TYPE 
             24              12 
[1] "6.0 - 31.1 (24.0)" "0.0 - 94.1 (12.0)"
[1] "hr=" "1.2"
D25V2, continuous
D25V3, binary
                 cls
clus                0   1
  KDM6A MUTATED     1   2
  KDM6A WILD-TYPE  90 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      1    2
  KDM6A WILD-TYPE   90  102
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             1              90
  MALE               2             102
[1] 2 2
[1] FALSE
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED       0                         0     3
  KDM6A WILD-TYPE     2                        15   173
D25V4, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0              15
  WHITE                                 3             173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   3
  KDM6A WILD-TYPE   3 186
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    3
  KDM6A WILD-TYPE    3  186
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             3             186
[1] 2 2
[1] FALSE
