[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTLAML-TB"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LAML-TB/10005979/LAML-TB.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/10667983/LAML-TB.mergedcluster.txt"

nPatients in clinical file=200, in cluster file=200, common to both=200
[1]   6 200
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
147  14  27   3 
  1   2   3   4 
147  14  27   3 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
48 45 65 14 22 
 1  2  3  4  5 
48 45 65 14 22 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
74 54 45 
 1  2  3 
74 54 45 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
16 14 15 58 26 44 
 1  2  3  4  5  6 
16 14 15 58 26 44 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
60 38 43 47 
 1  2  3  4 
60 38 43 47 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
70 35 83 
 1  2  3 
70 35 83 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "DCCUPLOADDATE"                   
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "KARNOFSKYPERFORMANCESCORE"       
[11] "RACE"                             "ETHNICITY"                       
[13] "BATCHNUMBER"                     

Input Data has 13 rows and 200 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 
          NA           NA         2557           NA           NA           NA 
TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2813 
        2861           NA           NA           NA           NA           NA 
TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 TCGA-AB-2818 TCGA-AB-2819 
          NA           NA           NA           NA           NA         2496 
TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2824 TCGA-AB-2825 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 
          NA           NA         2284           NA           NA           NA 
TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 
          NA           NA           NA         1673           NA           NA 
TCGA-AB-2838 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2843 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2848 TCGA-AB-2849 
          NA           NA           NA           NA           NA         2220 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2855 TCGA-AB-2856 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2857 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2861 TCGA-AB-2862 
          NA           NA           NA           NA           NA         1430 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2865 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2868 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
         243           NA          153          638          273          396 
TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2880 
         212         1219          638           NA          245          424 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2885 TCGA-AB-2886 
         393           NA          730           NA           NA          181 
TCGA-AB-2887 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2891 TCGA-AB-2892 
          NA          334          304           NA           NA          943 
TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 
          NA           NA           NA           NA          243          393 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2901 TCGA-AB-2903 TCGA-AB-2904 TCGA-AB-2905 
          NA           NA           59           NA           NA         1611 
TCGA-AB-2906 TCGA-AB-2907 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2911 
         577           NA           NA           30           NA         1186 
TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2917 
          NA         1216          792           NA          882         1216 
TCGA-AB-2918 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2921 TCGA-AB-2922 TCGA-AB-2923 
          NA           61           NA           NA           NA           NA 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2928 TCGA-AB-2929 
          90           NA           NA           NA           59           NA 
TCGA-AB-2930 TCGA-AB-2931 TCGA-AB-2932 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 
          NA           NA           NA           NA           28           NA 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2940 TCGA-AB-2941 
          59           NA           NA          455           NA           NA 
TCGA-AB-2942 TCGA-AB-2943 TCGA-AB-2944 TCGA-AB-2945 TCGA-AB-2946 TCGA-AB-2947 
         641           NA           NA           NA           NA           31 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 
          NA          699          306           NA         1492           NA 
TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 TCGA-AB-2964 TCGA-AB-2965 
          NA          609           NA           NA         1277           NA 
TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2971 
          NA         1035           NA         1127           NA           NA 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2975 TCGA-AB-2976 TCGA-AB-2977 
          NA           NA           NA           NA           NA           NA 
TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2981 TCGA-AB-2982 TCGA-AB-2983 
         699          671          699          487          150           NA 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
        1157           NA           NA           NA           NA           NA 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
         457         1826           NA           NA         1798         1551 
TCGA-AB-2996 TCGA-AB-2997 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 
        1581           NA           NA         1735         1249         1581 
TCGA-AB-3002 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 
          NA         2100           NA         1581           NA           NA 
TCGA-AB-3011 TCGA-AB-3012 
        1885         1887 
Variable 1:'AGE':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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] "rownames(nsurv.mat)"
[1] "AGE"       "GENDER"    "RACE"      "ETHNICITY"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 200 columns, 1 survival variables, and 4 non-survival variables.
AGE, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 54 76
  subtype2  3  8
  subtype3  4 21
  subtype4  1  1
subtype1 subtype2 subtype3 subtype4 
     130       11       25        2 
subtype1 subtype2 subtype3 subtype4 
      76        8       21        1 
$subtype1
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2810 
       26.04        84.07        31.07        94.06         2.04         1.02 
TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2817 
        7.99        12.03        26.04        27.02         8.05         8.98 
TCGA-AB-2818 TCGA-AB-2819 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2824 TCGA-AB-2825 
        9.96        82.06        27.02        31.99         0.99         6.97 
TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2831 TCGA-AB-2832 TCGA-AB-2834 
       24.03         8.98        75.09        21.04        12.00         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2844 
       55.00        17.03        15.98         0.92        46.06         4.01 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 
        9.99        46.09        14.96         2.01         7.96         2.93 
TCGA-AB-2854 TCGA-AB-2856 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2862 TCGA-AB-2863 
       12.03         4.93        18.97         9.99        47.01         1.02 
TCGA-AB-2864 TCGA-AB-2867 TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 
       18.97         6.05         7.99         5.03         5.03        20.98 
TCGA-AB-2873 TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2880 
        8.98        13.02         6.97        20.98         8.05        13.94 
TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2884 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 
       12.92        12.00        24.03         5.95        10.98         9.99 
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-2905 TCGA-AB-2906 TCGA-AB-2909 
       12.92        22.06         6.05        52.96        18.97         0.99 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2919 TCGA-AB-2924 
       38.99         9.01        39.98        26.04         2.01         2.96 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2928 TCGA-AB-2936 TCGA-AB-2937 
        7.99        15.02         2.96         1.94         1.94         7.07 
TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2954 
       21.07         7.99         1.02        22.98        10.06        49.05 
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-2969 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 
       37.05        26.04         0.99        20.02         3.02        30.08 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 
       22.98        22.98         4.93        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 

$subtype2
TCGA-AB-2805 TCGA-AB-2830 TCGA-AB-2866 TCGA-AB-2916 TCGA-AB-2923 TCGA-AB-2934 
       18.97         9.04         5.03        29.00         1.02         0.92 
TCGA-AB-2948 TCGA-AB-2964 TCGA-AB-2970 TCGA-AB-2977 TCGA-AB-2983 
       19.07        41.98        10.03         1.02        11.01 

$subtype3
TCGA-AB-2807 TCGA-AB-2813 TCGA-AB-2829 TCGA-AB-2838 TCGA-AB-2849 TCGA-AB-2855 
        5.95         1.02         8.98        12.00        72.99         6.97 
TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2865 TCGA-AB-2868 TCGA-AB-2878 TCGA-AB-2883 
       10.06        14.04         2.01         4.96        12.00        24.00 
TCGA-AB-2885 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2917 TCGA-AB-2920 
        7.04         1.94        17.00         1.02        39.98        12.03 
TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2938 TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2956 
        4.01         2.01         9.99         1.02        16.08         6.02 
TCGA-AB-2968 
       15.06 

$subtype4
TCGA-AB-2929 TCGA-AB-2939 
        4.04        14.96 

subtype1 subtype2 subtype3 subtype4 
    0.92     0.92     1.02     4.04 
subtype1 subtype2 subtype3 subtype4 
   94.06    41.98    72.99    14.96 
subtype1 subtype2 subtype3 subtype4 
   14.45    10.03     8.98     9.50 
[1] "0.9 - 94.1 (14.4)" "0.9 - 42.0 (10.0)" "1.0 - 73.0 (9.0)" 
[4] "4.0 - 15.0 (9.5)" 
[1] "Remove cluster labels:" "subtype4"              
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 73 74
  subtype2  6  8
  subtype3  6 21
  subtype4  2  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73   74
  subtype2    6    8
  subtype3    6   21
  subtype4    2    1
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       73        6        6        2
  MALE         74        8       21        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        11   132
  subtype2     0                         1    13
  subtype3     0                         2    25
  subtype4     0                         0     3
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        0        0        0
  BLACK OR AFRICAN AMERICAN       11        1        2        0
  WHITE                          132       13       25        3
[1] 3 4
[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
  subtype1   2 142
  subtype2   1  13
  subtype3   0  27
  subtype4   0   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  142
  subtype2    1   13
  subtype3    0   27
  subtype4    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        0        0
  NOT HISPANIC OR LATINO      142       13       27        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 12 30
  subtype2 29 13
  subtype3 12 43
  subtype4  6  7
  subtype5  4 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      42       42       55       13       17 
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       13       43        7       13 
$subtype1
TCGA-AB-2802 TCGA-AB-2809 TCGA-AB-2811 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2824 
       12.00         2.04         7.99         8.05         9.96         0.99 
TCGA-AB-2825 TCGA-AB-2832 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2848 TCGA-AB-2851 
        6.97        12.00        55.00        17.03        14.96         7.96 
TCGA-AB-2853 TCGA-AB-2869 TCGA-AB-2879 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 
        2.93         7.99         8.05        24.00        24.03         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2911 TCGA-AB-2924 TCGA-AB-2925 
        5.95         5.03         7.04        38.99         2.96         7.99 
TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2956 TCGA-AB-2963 TCGA-AB-2965 TCGA-AB-2967 
        7.99         1.02         6.02        53.98        11.01        34.03 
TCGA-AB-2969 TCGA-AB-2972 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2981 TCGA-AB-2985 
       37.05         0.99         3.02        30.08        16.01         8.98 
TCGA-AB-2986 TCGA-AB-2988 TCGA-AB-2993 TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3011 
        6.97         0.99        25.02        69.04        15.95        61.97 

$subtype2
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2815 TCGA-AB-2819 
       26.04        84.07        31.07        94.06        27.02        82.06 
TCGA-AB-2828 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2858 
       75.09         0.92        46.06         9.99        46.09        18.97 
TCGA-AB-2862 TCGA-AB-2870 TCGA-AB-2872 TCGA-AB-2875 TCGA-AB-2880 TCGA-AB-2881 
       47.01         5.03        20.98         6.97        13.94        12.92 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2892 TCGA-AB-2897 TCGA-AB-2906 
        5.95        10.98         9.99        31.00         7.99        18.97 
TCGA-AB-2909 TCGA-AB-2914 TCGA-AB-2937 TCGA-AB-2942 TCGA-AB-2950 TCGA-AB-2954 
        0.99        26.04         7.07        21.07        10.06        49.05 
TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2991 
       16.08        20.02        22.06        22.98         4.93        60.03 
TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3007 TCGA-AB-3012 
        1.02        57.04        41.06        51.98        51.98        62.04 

$subtype3
TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2817 TCGA-AB-2821 
       18.97         5.95         1.02        26.04         8.98        27.02 
TCGA-AB-2822 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2833 TCGA-AB-2838 
       31.99         8.98         9.04        21.04        14.99        12.00 
TCGA-AB-2843 TCGA-AB-2847 TCGA-AB-2854 TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2863 
        7.07        19.99        12.03        10.06        14.04         1.02 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2871 TCGA-AB-2873 TCGA-AB-2878 TCGA-AB-2882 
        6.05         4.96         5.03         8.98        12.00        12.00 
TCGA-AB-2885 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2908 
        7.04        12.92        22.06         1.94        17.00         1.02 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2928 
       29.00        39.98        12.03        15.02         2.96         1.94 
TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2938 
        4.04         4.01         0.92         2.01         1.94         9.99 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-2959 TCGA-AB-2968 TCGA-AB-2971 
       19.07        22.98         1.02        16.08        15.06        26.04 
TCGA-AB-2978 TCGA-AB-2983 TCGA-AB-2987 TCGA-AB-2992 TCGA-AB-2995 TCGA-AB-2996 
       22.98        11.01         6.05        56.09        50.99        51.98 
TCGA-AB-3002 
       47.05 

$subtype4
TCGA-AB-2810 TCGA-AB-2826 TCGA-AB-2866 TCGA-AB-2874 TCGA-AB-2877 TCGA-AB-2900 
        1.02        24.03         5.03        13.02        20.98         6.05 
TCGA-AB-2919 TCGA-AB-2923 TCGA-AB-2964 TCGA-AB-2973 TCGA-AB-2977 TCGA-AB-2984 
        2.01         1.02        41.98        20.02         1.02        38.04 
TCGA-AB-2990 
       15.02 

$subtype5
TCGA-AB-2812 TCGA-AB-2827 TCGA-AB-2834 TCGA-AB-2839 TCGA-AB-2844 TCGA-AB-2849 
       12.03         8.98         8.05        15.98         4.01        72.99 
TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2876 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2939 
        6.97         4.93        40.08         9.01        39.98        14.96 
TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2989 TCGA-AB-3008 TCGA-AB-3009 
       28.08        10.03        12.00        27.02        18.97 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.99     0.92     0.92     1.02     4.01 
subtype1 subtype2 subtype3 subtype4 subtype5 
   69.04    94.06    56.09    41.98    72.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
   8.050   21.565   12.000   13.020   12.030 
[1] "1.0 - 69.0 (8.1)"  "0.9 - 94.1 (21.6)" "0.9 - 56.1 (12.0)"
[4] "1.0 - 42.0 (13.0)" "4.0 - 73.0 (12.0)"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 24 24
  subtype2 24 21
  subtype3 26 39
  subtype4  8  6
  subtype5  7 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   24
  subtype2   24   21
  subtype3   26   39
  subtype4    8    6
  subtype5    7   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       24       24       26        8        7
  MALE         24       21       39        6       15
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    45
  subtype2     1                         2    41
  subtype3     0                         6    59
  subtype4     0                         2    12
  subtype5     0                         1    20
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        0        0
  BLACK OR AFRICAN AMERICAN        2        2        6        2        1
  WHITE                           45       41       59       12       20
[1] 3 5
[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
  subtype1  0 48
  subtype2  0 44
  subtype3  1 63
  subtype4  0 14
  subtype5  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   48
  subtype2    0   44
  subtype3    1   63
  subtype4    0   14
  subtype5    0   21
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        1        0        0
  NOT HISPANIC OR LATINO       48       44       63       14       21
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 26 39
  subtype2 17 31
  subtype3 14 24
subtype1 subtype2 subtype3 
      65       48       38 
subtype1 subtype2 subtype3 
      39       31       24 
$subtype1
TCGA-AB-2803 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2814 TCGA-AB-2817 
       26.04        31.07         5.95        94.06        26.04         8.98 
TCGA-AB-2819 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2830 TCGA-AB-2838 TCGA-AB-2843 
       82.06        27.02        31.99         9.04        12.00         7.07 
TCGA-AB-2845 TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2854 TCGA-AB-2857 TCGA-AB-2858 
        9.99        19.99        72.99        12.03        10.06        18.97 
TCGA-AB-2860 TCGA-AB-2863 TCGA-AB-2865 TCGA-AB-2868 TCGA-AB-2872 TCGA-AB-2875 
       14.04         1.02         2.01         4.96        20.98         6.97 
TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 
       12.00         7.04         5.95        12.92        22.06         1.94 
TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2917 TCGA-AB-2927 TCGA-AB-2929 
       17.00         1.02         0.99        39.98         2.96         4.04 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2949 
        2.01         1.94         7.07         9.99        14.96        22.98 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2959 TCGA-AB-2964 TCGA-AB-2966 
       10.06         1.02        16.08        16.08        41.98        28.08 
TCGA-AB-2970 TCGA-AB-2978 TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 
       10.03        22.98        22.06        22.98         4.93        11.01 
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-3008 TCGA-AB-3009 TCGA-AB-3012 
       51.98        47.05        27.02        18.97        62.04 

$subtype2
TCGA-AB-2805 TCGA-AB-2811 TCGA-AB-2813 TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2818 
       18.97         7.99         1.02        27.02         8.05         9.96 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2828 TCGA-AB-2833 TCGA-AB-2834 
        0.99         6.97        24.03        75.09        14.99         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2851 TCGA-AB-2856 
       55.00        17.03         4.01        46.09         7.96         4.93 
TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2870 TCGA-AB-2873 TCGA-AB-2880 TCGA-AB-2881 
        5.03         6.05         5.03         8.98        13.94        12.92 
TCGA-AB-2884 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2900 TCGA-AB-2911 TCGA-AB-2912 
       24.03        10.98         9.99         6.05        38.99         9.01 
TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2933 TCGA-AB-2934 
       26.04        29.00         2.96         7.99         4.01         0.92 
TCGA-AB-2942 TCGA-AB-2948 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2965 TCGA-AB-2967 
       21.07        19.07        49.05         6.02        11.01        34.03 
TCGA-AB-2969 TCGA-AB-2973 TCGA-AB-2981 TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-3005 
       37.05        20.02        16.01         8.98         6.05        69.04 

$subtype3
TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2832 TCGA-AB-2839 TCGA-AB-2840 TCGA-AB-2841 
        1.02        12.03        12.00        15.98         0.92        46.06 
TCGA-AB-2848 TCGA-AB-2853 TCGA-AB-2855 TCGA-AB-2859 TCGA-AB-2862 TCGA-AB-2869 
       14.96         2.93         6.97         9.99        47.01         7.99 
TCGA-AB-2871 TCGA-AB-2874 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2895 TCGA-AB-2896 
        5.03        13.02        20.98         8.05         5.03         7.04 
TCGA-AB-2897 TCGA-AB-2913 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2928 TCGA-AB-2963 
        7.99        39.98         2.01        12.03         1.94        53.98 
TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2984 TCGA-AB-2986 
       26.04         0.99        30.08         1.02        38.04         6.97 
TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2998 TCGA-AB-3006 
        0.99        15.02        25.02        59.11         1.02        15.95 
TCGA-AB-3007 TCGA-AB-3011 
       51.98        61.97 

subtype1 subtype2 subtype3 
    0.99     0.92     0.92 
subtype1 subtype2 subtype3 
   94.06    75.09    61.97 
subtype1 subtype2 subtype3 
  16.080   10.485   12.015 
[1] "1.0 - 94.1 (16.1)" "0.9 - 75.1 (10.5)" "0.9 - 62.0 (12.0)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 31 43
  subtype2 22 32
  subtype3 27 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   43
  subtype2   22   32
  subtype3   27   18
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       31       22       27
  MALE         43       32       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    68
  subtype2     1                         2    51
  subtype3     0                         8    37
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        3        2        8
  WHITE                           68       51       37
[1] 3 3
[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
  subtype1  0 71
  subtype2  1 53
  subtype3  0 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   71
  subtype2    1   53
  subtype3    0   45
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        0
  NOT HISPANIC OR LATINO       71       53       45
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 11  4
  subtype2  9  5
  subtype3  7  6
  subtype4 12 38
  subtype5 10 13
  subtype6  8 28
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      15       14       13       50       23       36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        5        6       38       13       28 
$subtype1
TCGA-AB-2803 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2862 TCGA-AB-2872 TCGA-AB-2897 
       26.04         0.92        46.06        47.01        20.98         7.99 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2991 TCGA-AB-2994 TCGA-AB-2998 TCGA-AB-2999 
       22.98         4.93        60.03        59.11         1.02        57.04 
TCGA-AB-3001 TCGA-AB-3007 TCGA-AB-3012 
       51.98        51.98        62.04 

$subtype2
TCGA-AB-2805 TCGA-AB-2815 TCGA-AB-2828 TCGA-AB-2833 TCGA-AB-2846 TCGA-AB-2870 
       18.97        27.02        75.09        14.99        46.09         5.03 
TCGA-AB-2881 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2934 
       12.92        10.98         9.99        26.04        29.00         0.92 
TCGA-AB-2942 TCGA-AB-2954 
       21.07        49.05 

$subtype3
TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2819 TCGA-AB-2845 TCGA-AB-2858 TCGA-AB-2875 
       31.07        94.06        82.06         9.99        18.97         6.97 
TCGA-AB-2880 TCGA-AB-2886 TCGA-AB-2937 TCGA-AB-2950 TCGA-AB-2979 TCGA-AB-3000 
       13.94         5.95         7.07        10.06        22.06        41.06 
TCGA-AB-3008 
       27.02 

$subtype4
TCGA-AB-2807 TCGA-AB-2814 TCGA-AB-2817 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2830 
        5.95        26.04         8.98        27.02        31.99         9.04 
TCGA-AB-2838 TCGA-AB-2843 TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2854 TCGA-AB-2855 
       12.00         7.07        19.99        72.99        12.03         6.97 
TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2863 TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 
       10.06        14.04         1.02         2.01         6.05         4.96 
TCGA-AB-2874 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 
       13.02        12.00         7.04        12.92        22.06         1.94 
TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2912 TCGA-AB-2917 TCGA-AB-2920 
       17.00         1.02         0.99         9.01        39.98        12.03 
TCGA-AB-2927 TCGA-AB-2928 TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2935 TCGA-AB-2936 
        2.96         1.94         4.04         4.01         2.01         1.94 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2959 
        9.99        14.96        22.98         1.02        16.08        16.08 
TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2978 TCGA-AB-2983 TCGA-AB-2995 TCGA-AB-2996 
       28.08        10.03        22.98        11.01        50.99        51.98 
TCGA-AB-3002 TCGA-AB-3009 
       47.05        18.97 

$subtype5
TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2839 TCGA-AB-2853 TCGA-AB-2859 TCGA-AB-2869 
        1.02        12.03        15.98         2.93         9.99         7.99 
TCGA-AB-2871 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2913 
        5.03        20.98         8.05         5.03         7.04        39.98 
TCGA-AB-2919 TCGA-AB-2964 TCGA-AB-2972 TCGA-AB-2976 TCGA-AB-2984 TCGA-AB-2986 
        2.01        41.98         0.99        30.08        38.04         6.97 
TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2993 TCGA-AB-3006 TCGA-AB-3011 
        0.99        15.02        25.02        15.95        61.97 

$subtype6
TCGA-AB-2811 TCGA-AB-2813 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2824 TCGA-AB-2825 
        7.99         1.02         8.05         9.96         0.99         6.97 
TCGA-AB-2826 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2844 
       24.03        12.00         8.05        55.00        17.03         4.01 
TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2856 TCGA-AB-2866 TCGA-AB-2873 TCGA-AB-2884 
       14.96         7.96         4.93         5.03         8.98        24.03 
TCGA-AB-2900 TCGA-AB-2911 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2948 TCGA-AB-2956 
        6.05        38.99         2.96         7.99        19.07         6.02 
TCGA-AB-2963 TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2973 
       53.98        11.01        34.03        37.05        26.04        20.02 
TCGA-AB-2977 TCGA-AB-2981 TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-2992 TCGA-AB-3005 
        1.02        16.01         8.98         6.05        56.09        69.04 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.92     0.92     5.95     0.99     0.99     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   62.04    75.09    94.06    72.99    61.97    69.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  46.060   20.020   18.970   11.505    9.990    9.470 
[1] "0.9 - 62.0 (46.1)" "0.9 - 75.1 (20.0)" "6.0 - 94.1 (19.0)"
[4] "1.0 - 73.0 (11.5)" "1.0 - 62.0 (10.0)" "1.0 - 69.0 (9.5)" 
D4V2, continuous
D4V3, binary
          cls
clus        0  1
  subtype1  9  7
  subtype2  6  8
  subtype3  6  9
  subtype4 22 36
  subtype5 16 10
  subtype6 21 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    7
  subtype2    6    8
  subtype3    6    9
  subtype4   22   36
  subtype5   16   10
  subtype6   21   23
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        9        6        6       22       16       21
  MALE          7        8        9       36       10       23
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    13
  subtype2     0                         0    14
  subtype3     0                         0    15
  subtype4     1                         3    53
  subtype5     0                         6    20
  subtype6     1                         2    41
D4V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        1        0
  BLACK OR AFRICAN AMERICAN        2        0        0        3        6
  WHITE                           13       14       15       53       20
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           41
[1] 3 6
[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
  subtype1  0 15
  subtype2  1 13
  subtype3  0 15
  subtype4  0 56
  subtype5  0 26
  subtype6  0 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   15
  subtype2    1   13
  subtype3    0   15
  subtype4    0   56
  subtype5    0   26
  subtype6    0   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        0        0        0
  NOT HISPANIC OR LATINO       15       13       15       56       26       44
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 15 38
  subtype2 16 18
  subtype3 12 23
  subtype4 19 23
subtype1 subtype2 subtype3 subtype4 
      53       34       35       42 
subtype1 subtype2 subtype3 subtype4 
      38       18       23       23 
$subtype1
TCGA-AB-2802 TCGA-AB-2811 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2824 TCGA-AB-2825 
       12.00         7.99         8.05         9.96         0.99         6.97 
TCGA-AB-2826 TCGA-AB-2830 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 
       24.03         9.04        12.00         8.05        55.00        17.03 
TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2866 TCGA-AB-2869 
       14.96         7.96         6.97         4.93         5.03         7.99 
TCGA-AB-2871 TCGA-AB-2873 TCGA-AB-2877 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 
        5.03         8.98        20.98        24.00        24.03         6.97 
TCGA-AB-2894 TCGA-AB-2896 TCGA-AB-2900 TCGA-AB-2911 TCGA-AB-2916 TCGA-AB-2923 
        5.95         7.04         6.05        38.99        29.00         1.02 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2933 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 
        2.96         7.99         4.01         7.99         1.02        19.07 
TCGA-AB-2956 TCGA-AB-2963 TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2971 
        6.02        53.98        11.01        34.03        37.05        26.04 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2976 TCGA-AB-2981 TCGA-AB-2985 TCGA-AB-2987 
        0.99        20.02        30.08        16.01         8.98         6.05 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-3005 TCGA-AB-3006 
        0.99        12.00        15.02        69.04        15.95 

$subtype2
TCGA-AB-2803 TCGA-AB-2821 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2843 
       26.04        27.02        12.00         0.92        46.06         7.07 
TCGA-AB-2857 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 
       10.06         9.99        14.04         2.01         6.05         4.96 
TCGA-AB-2872 TCGA-AB-2878 TCGA-AB-2885 TCGA-AB-2888 TCGA-AB-2897 TCGA-AB-2898 
       20.98        12.00         7.04        10.98         7.99        12.92 
TCGA-AB-2917 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2939 TCGA-AB-2949 TCGA-AB-2952 
       39.98         4.04         2.01        14.96        22.98         1.02 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2994 TCGA-AB-2995 
       22.98        22.98        60.03        56.09        59.11        50.99 
TCGA-AB-2999 TCGA-AB-3001 TCGA-AB-3007 TCGA-AB-3012 
       57.04        51.98        51.98        62.04 

$subtype3
TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2813 TCGA-AB-2815 TCGA-AB-2817 
       18.97         5.95        94.06         1.02        27.02         8.98 
TCGA-AB-2819 TCGA-AB-2828 TCGA-AB-2833 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 
       82.06        75.09        14.99         9.99        46.09        19.99 
TCGA-AB-2854 TCGA-AB-2862 TCGA-AB-2870 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2892 
       12.03        47.01         5.03        12.92        12.00        31.00 
TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2908 TCGA-AB-2912 TCGA-AB-2927 TCGA-AB-2936 
       22.06         1.94         1.02         9.01         2.96         1.94 
TCGA-AB-2938 TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2959 TCGA-AB-2970 TCGA-AB-2982 
        9.99        10.06        49.05        16.08        10.03         4.93 
TCGA-AB-2983 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-3002 TCGA-AB-3008 
       11.01        51.98         1.02        47.05        27.02 

$subtype4
TCGA-AB-2806 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2822 TCGA-AB-2839 
       31.07         1.02        12.03        26.04        31.99        15.98 
TCGA-AB-2844 TCGA-AB-2849 TCGA-AB-2853 TCGA-AB-2858 TCGA-AB-2863 TCGA-AB-2874 
        4.01        72.99         2.93        18.97         1.02        13.02 
TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2879 TCGA-AB-2880 TCGA-AB-2886 TCGA-AB-2889 
        6.97        40.08         8.05        13.94         5.95         9.99 
TCGA-AB-2895 TCGA-AB-2904 TCGA-AB-2909 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2919 
        5.03        17.00         0.99        39.98        26.04         2.01 
TCGA-AB-2920 TCGA-AB-2926 TCGA-AB-2928 TCGA-AB-2934 TCGA-AB-2937 TCGA-AB-2942 
       12.03        15.02         1.94         0.92         7.07        21.07 
TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2964 TCGA-AB-2966 TCGA-AB-2977 TCGA-AB-2979 
       16.08        20.02        41.98        28.08         1.02        22.06 
TCGA-AB-2984 TCGA-AB-2986 TCGA-AB-2993 TCGA-AB-3000 TCGA-AB-3009 TCGA-AB-3011 
       38.04         6.97        25.02        41.06        18.97        61.97 

subtype1 subtype2 subtype3 subtype4 
    0.99     0.92     1.02     0.92 
subtype1 subtype2 subtype3 subtype4 
   69.04    62.04    94.06    72.99 
subtype1 subtype2 subtype3 subtype4 
    8.98    14.50    12.03    15.50 
[1] "1.0 - 69.0 (9.0)"  "0.9 - 62.0 (14.5)" "1.0 - 94.1 (12.0)"
[4] "0.9 - 73.0 (15.5)"
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 26 34
  subtype2 17 21
  subtype3 21 22
  subtype4 23 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   34
  subtype2   17   21
  subtype3   21   22
  subtype4   23   24
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       26       17       21       23
  MALE         34       21       22       24
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4    55
  subtype2     0                         2    36
  subtype3     0                         2    40
  subtype4     1                         5    40
D5V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        1
  BLACK OR AFRICAN AMERICAN        4        2        2        5
  WHITE                           55       36       40       40
[1] 3 4
[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
  subtype1  1 59
  subtype2  0 38
  subtype3  0 41
  subtype4  0 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   59
  subtype2    0   38
  subtype3    0   41
  subtype4    0   46
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        0        0
  NOT HISPANIC OR LATINO       59       38       41       46
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 20 42
  subtype2 14 16
  subtype3 28 44
subtype1 subtype2 subtype3 
      62       30       72 
subtype1 subtype2 subtype3 
      42       16       44 
$subtype1
TCGA-AB-2802 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2816 TCGA-AB-2818 
       12.00         1.02         7.99        12.03         8.05         9.96 
TCGA-AB-2824 TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2832 TCGA-AB-2834 TCGA-AB-2835 
        0.99         6.97        24.03        12.00         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2839 TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2856 
       17.03        15.98        14.96         7.96         2.93         4.93 
TCGA-AB-2866 TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2873 TCGA-AB-2877 TCGA-AB-2879 
        5.03         7.99         5.03         8.98        20.98         8.05 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 
       24.00        24.03         6.97         5.95         5.03         7.04 
TCGA-AB-2900 TCGA-AB-2911 TCGA-AB-2913 TCGA-AB-2919 TCGA-AB-2923 TCGA-AB-2924 
        6.05        38.99        39.98         2.01         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2956 TCGA-AB-2963 TCGA-AB-2964 
        7.99         7.99         1.02         6.02        53.98        41.98 
TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2973 
       11.01        34.03        37.05        26.04         0.99        20.02 
TCGA-AB-2976 TCGA-AB-2981 TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 
       30.08        16.01        38.04         8.98         6.97         6.05 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-3005 
        0.99        12.00        15.02        56.09        25.02        69.04 
TCGA-AB-3006 TCGA-AB-3011 
       15.95        61.97 

$subtype2
TCGA-AB-2803 TCGA-AB-2814 TCGA-AB-2821 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 
       26.04        26.04        27.02        12.00         0.92        46.06 
TCGA-AB-2843 TCGA-AB-2857 TCGA-AB-2859 TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 
        7.07        10.06         9.99         2.01         6.05         4.96 
TCGA-AB-2872 TCGA-AB-2878 TCGA-AB-2885 TCGA-AB-2888 TCGA-AB-2897 TCGA-AB-2929 
       20.98        12.00         7.04        10.98         7.99         4.04 
TCGA-AB-2935 TCGA-AB-2939 TCGA-AB-2949 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2991 
        2.01        14.96        22.98        22.98        22.98        60.03 
TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2999 TCGA-AB-3001 TCGA-AB-3007 TCGA-AB-3012 
       59.11        50.99        57.04        51.98        51.98        62.04 

$subtype3
TCGA-AB-2805 TCGA-AB-2806 TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2813 TCGA-AB-2815 
       18.97        31.07         5.95        94.06         1.02        27.02 
TCGA-AB-2817 TCGA-AB-2819 TCGA-AB-2822 TCGA-AB-2828 TCGA-AB-2830 TCGA-AB-2833 
        8.98        82.06        31.99        75.09         9.04        14.99 
TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2854 
        4.01         9.99        46.09        19.99        72.99        12.03 
TCGA-AB-2855 TCGA-AB-2858 TCGA-AB-2860 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2870 
        6.97        18.97        14.04        47.01         1.02         5.03 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2880 TCGA-AB-2881 TCGA-AB-2882 
       13.02         6.97        40.08        13.94        12.92        12.00 
TCGA-AB-2886 TCGA-AB-2889 TCGA-AB-2892 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 
        5.95         9.99        31.00        12.92        22.06         1.94 
TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2916 
       17.00         1.02         0.99         9.01        26.04        29.00 
TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2928 TCGA-AB-2933 
       39.98        12.03        15.02         2.96         1.94         4.01 
TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2942 TCGA-AB-2948 
        0.92         1.94         7.07         9.99        21.07        19.07 
TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2959 
       10.06         1.02        49.05        16.08        20.02        16.08 
TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2982 TCGA-AB-2983 
       28.08        10.03         1.02        22.06         4.93        11.01 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-3000 TCGA-AB-3002 TCGA-AB-3008 TCGA-AB-3009 
       51.98         1.02        41.06        47.05        27.02        18.97 

subtype1 subtype2 subtype3 
    0.99     0.92     0.92 
subtype1 subtype2 subtype3 
   69.04    62.04    94.06 
subtype1 subtype2 subtype3 
    9.47    17.97    13.48 
[1] "1.0 - 69.0 (9.5)"  "0.9 - 62.0 (18.0)" "0.9 - 94.1 (13.5)"
D6V2, continuous
D6V3, binary
          cls
clus        0  1
  subtype1 36 34
  subtype2 13 22
  subtype3 38 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   34
  subtype2   13   22
  subtype3   38   45
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       36       13       38
  MALE         34       22       45
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    63
  subtype2     0                         2    33
  subtype3     1                         5    75
D6V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        0        1
  BLACK OR AFRICAN AMERICAN        6        2        5
  WHITE                           63       33       75
[1] 3 3
[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
  subtype1  0 70
  subtype2  0 35
  subtype3  1 79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   70
  subtype2    0   35
  subtype3    1   79
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        0        1
  NOT HISPANIC OR LATINO       70       35       79
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
