[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/22506504/LAML-TB.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/22541002/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 
49 44 55 43 
 1  2  3  4 
49 44 55 43 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5 
25 25 62 38 44 
 1  2  3  4  5 
25 25 62 38 44 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
75 52 46 
 1  2  3 
75 52 46 
[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  5 
60 31 43 33 21 
 1  2  3  4  5 
60 31 43 33 21 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
70 35 83 
 1  2  3 
70 35 83 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "DAYS_TO_LAST_KNOWN_ALIVE"            
 [9] "KARNOFSKY_PERFORMANCE_SCORE"         
[10] "RACE"                                
[11] "ETHNICITY"                           

Input Data has 11 rows and 200 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=62,	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=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "KARNOFSKY_PERFORMANCE_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 200 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 14 34
  subtype2 13 29
  subtype3 19 29
  subtype4 16 24
subtype1 subtype2 subtype3 subtype4 
      48       42       48       40 
subtype1 subtype2 subtype3 subtype4 
      34       29       29       24 
$subtype1
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2809 TCGA-AB-2812 TCGA-AB-2816 TCGA-AB-2818 
       26.04        84.07         2.04        12.03         8.05         9.96 
TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2831 
       27.02        31.99         0.00        24.03         8.98        21.04 
TCGA-AB-2832 TCGA-AB-2836 TCGA-AB-2839 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       12.00        17.03        15.98         9.99        46.09        14.96 
TCGA-AB-2850 TCGA-AB-2853 TCGA-AB-2858 TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 
        2.01         2.93        18.97         9.99         0.00        47.01 
TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2866 TCGA-AB-2884 TCGA-AB-2889 TCGA-AB-2903 
        1.02        18.97         5.03        24.03         9.99         0.00 
TCGA-AB-2905 TCGA-AB-2915 TCGA-AB-2942 TCGA-AB-2947 TCGA-AB-2971 TCGA-AB-2972 
       52.96         0.00        21.07         1.02        26.04         0.99 
TCGA-AB-2986 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 
        6.97        15.02        60.03        56.09        25.02        59.11 
TCGA-AB-2999 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3007 TCGA-AB-3011 TCGA-AB-3012 
       57.04        51.98        47.05        51.98        61.97        62.04 

$subtype2
TCGA-AB-2805 TCGA-AB-2811 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2819 TCGA-AB-2825 
       18.97         7.99         1.02        26.04        82.06         6.97 
TCGA-AB-2829 TCGA-AB-2835 TCGA-AB-2849 TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2857 
        8.98        55.00        72.99         6.97         4.93        10.06 
TCGA-AB-2860 TCGA-AB-2865 TCGA-AB-2869 TCGA-AB-2873 TCGA-AB-2883 TCGA-AB-2885 
       14.04         2.01         7.99         8.98        24.00         7.04 
TCGA-AB-2899 TCGA-AB-2900 TCGA-AB-2904 TCGA-AB-2910 TCGA-AB-2914 TCGA-AB-2920 
       22.06         6.05        17.00         0.00        26.04        12.03 
TCGA-AB-2922 TCGA-AB-2924 TCGA-AB-2941 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2963 
        0.00         2.96         0.00        10.06         1.02        53.98 
TCGA-AB-2964 TCGA-AB-2965 TCGA-AB-2973 TCGA-AB-2977 TCGA-AB-2980 TCGA-AB-2982 
       41.98        11.01        20.02         1.02        22.98         4.93 
TCGA-AB-2983 TCGA-AB-2985 TCGA-AB-2988 TCGA-AB-3005 TCGA-AB-3008 TCGA-AB-3009 
       11.01         8.98         0.99        69.04        27.02        18.97 

$subtype3
TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2820 TCGA-AB-2824 TCGA-AB-2830 TCGA-AB-2842 
       31.07        94.06         0.00         0.99         9.04         0.00 
TCGA-AB-2868 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2875 TCGA-AB-2877 
        4.96         5.03         5.03        20.98         6.97        20.98 
TCGA-AB-2881 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
       12.92         5.95        10.98         0.00        31.00         6.97 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2901 TCGA-AB-2906 
        5.03         7.04         7.99        12.92         1.94        18.97 
TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2916 
        1.02         0.99        38.99         9.01        39.98        29.00 
TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 
        7.99        15.02         2.96         0.00         4.01         0.92 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2948 TCGA-AB-2955 TCGA-AB-2959 
        1.94         7.07         9.99        19.07        16.08        16.08 
TCGA-AB-2966 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2987 TCGA-AB-2989 TCGA-AB-3006 
       28.08         3.02        30.08         6.05        12.00        15.95 

$subtype4
TCGA-AB-2807 TCGA-AB-2810 TCGA-AB-2815 TCGA-AB-2817 TCGA-AB-2828 TCGA-AB-2834 
        5.95         1.02        27.02         8.98        75.09         8.05 
TCGA-AB-2837 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2844 TCGA-AB-2851 
        0.00        12.00         0.92        46.06         4.01         7.96 
TCGA-AB-2854 TCGA-AB-2867 TCGA-AB-2874 TCGA-AB-2878 TCGA-AB-2879 TCGA-AB-2882 
       12.03         6.05        13.02        12.00         8.05        12.00 
TCGA-AB-2894 TCGA-AB-2917 TCGA-AB-2919 TCGA-AB-2923 TCGA-AB-2929 TCGA-AB-2935 
        5.95        39.98         2.01         1.02         4.04         2.01 
TCGA-AB-2939 TCGA-AB-2945 TCGA-AB-2949 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 
       14.96         7.99        22.98        49.05         6.02        20.02 
TCGA-AB-2967 TCGA-AB-2968 TCGA-AB-2969 TCGA-AB-2970 TCGA-AB-2978 TCGA-AB-2984 
       34.03        15.06        37.05        10.03        22.98        38.04 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-3000 
       50.99        51.98         1.02        41.06 

subtype1 subtype2 subtype3 subtype4 
       0        0        0        0 
subtype1 subtype2 subtype3 subtype4 
   84.07    82.06    94.06    75.09 
subtype1 subtype2 subtype3 subtype4 
   18.00    10.06     7.99    12.00 
[1] "0.0 - 84.1 (18.0)" "0.0 - 82.1 (10.1)" "0.0 - 94.1 (8.0)" 
[4] "0.0 - 75.1 (12.0)"
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 27 22
  subtype2 18 26
  subtype3 21 34
  subtype4 21 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   22
  subtype2   18   26
  subtype3   21   34
  subtype4   21   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       27       18       21       21
  MALE         22       26       34       22
[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    44
  subtype2     0                         4    38
  subtype3     1                         4    50
  subtype4     0                         2    41
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        1        0
  BLACK OR AFRICAN AMERICAN        4        4        4        2
  WHITE                           44       38       50       41
[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 47
  subtype2  0 42
  subtype3  1 54
  subtype4  0 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   47
  subtype2    0   42
  subtype3    1   54
  subtype4    0   42
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        0        1        0
  NOT HISPANIC OR LATINO       47       42       54       42
[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  5 20
  subtype2 16  8
  subtype3 11 45
  subtype4 21 13
  subtype5 10 30
subtype1 subtype2 subtype3 subtype4 subtype5 
      25       24       56       34       40 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20        8       45       13       30 
$subtype1
TCGA-AB-2802 TCGA-AB-2809 TCGA-AB-2811 TCGA-AB-2825 TCGA-AB-2832 TCGA-AB-2853 
       12.00         2.04         7.99         6.97        12.00         2.93 
TCGA-AB-2861 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2895 
        0.00        24.00        24.03         6.97         5.95         5.03 
TCGA-AB-2896 TCGA-AB-2910 TCGA-AB-2925 TCGA-AB-2931 TCGA-AB-2945 TCGA-AB-2947 
        7.04         0.00         7.99         0.00         7.99         1.02 
TCGA-AB-2956 TCGA-AB-2965 TCGA-AB-2969 TCGA-AB-2974 TCGA-AB-2981 TCGA-AB-2987 
        6.02        11.01        37.05         3.02        16.01         6.05 
TCGA-AB-3005 
       69.04 

$subtype2
TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2810 TCGA-AB-2822 TCGA-AB-2823 TCGA-AB-2840 
       26.04        84.07         1.02        31.99         0.00         0.92 
TCGA-AB-2841 TCGA-AB-2845 TCGA-AB-2862 TCGA-AB-2872 TCGA-AB-2874 TCGA-AB-2897 
       46.06         9.99        47.01        20.98        13.02         7.99 
TCGA-AB-2906 TCGA-AB-2919 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2984 TCGA-AB-2990 
       18.97         2.01        22.98         4.93        38.04        15.02 
TCGA-AB-2991 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3007 TCGA-AB-3011 TCGA-AB-3012 
       60.03         1.02        57.04        51.98        61.97        62.04 

$subtype3
TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2817 TCGA-AB-2820 
       18.97         5.95         1.02        26.04         8.98         0.00 
TCGA-AB-2821 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 TCGA-AB-2838 TCGA-AB-2843 
       27.02         8.98         9.04        21.04        12.00         7.07 
TCGA-AB-2847 TCGA-AB-2854 TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2863 TCGA-AB-2867 
       19.99        12.03        10.06        14.04         1.02         6.05 
TCGA-AB-2868 TCGA-AB-2873 TCGA-AB-2878 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2890 
        4.96         8.98        12.00        12.00         7.04         0.00 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2915 
       12.92        22.06         1.94        17.00         1.02         0.00 
TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2929 
       39.98        12.03         0.00        15.02         2.96         4.04 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2938 TCGA-AB-2941 
        4.01         0.92         2.01         1.94         9.99         0.00 
TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-2959 TCGA-AB-2964 TCGA-AB-2968 
       19.07        22.98         1.02        16.08        41.98        15.06 
TCGA-AB-2971 TCGA-AB-2977 TCGA-AB-2978 TCGA-AB-2983 TCGA-AB-2992 TCGA-AB-2995 
       26.04         1.02        22.98        11.01        56.09        50.99 
TCGA-AB-2996 TCGA-AB-3002 
       51.98        47.05 

$subtype4
TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2815 TCGA-AB-2819 TCGA-AB-2828 TCGA-AB-2833 
       31.07        94.06        27.02        82.06        75.09        14.99 
TCGA-AB-2846 TCGA-AB-2849 TCGA-AB-2855 TCGA-AB-2858 TCGA-AB-2870 TCGA-AB-2875 
       46.09        72.99         6.97        18.97         5.03         6.97 
TCGA-AB-2881 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2892 TCGA-AB-2909 
       12.92         5.95        10.98         9.99        31.00         0.99 
TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2916 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2942 
        9.01        26.04        29.00         7.07        14.96        21.07 
TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2966 TCGA-AB-2979 
       10.06        49.05        16.08        20.02        28.08        22.06 
TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3008 TCGA-AB-3009 
       41.06        51.98        27.02        18.97 

$subtype5
TCGA-AB-2812 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2824 TCGA-AB-2826 TCGA-AB-2827 
       12.03         8.05         9.96         0.99        24.03         8.98 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2842 
        8.05        55.00        17.03         0.00        15.98         0.00 
TCGA-AB-2844 TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2856 TCGA-AB-2866 TCGA-AB-2869 
        4.01        14.96         7.96         4.93         5.03         7.99 
TCGA-AB-2871 TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2900 TCGA-AB-2903 
        5.03        40.08        20.98         8.05         6.05         0.00 
TCGA-AB-2911 TCGA-AB-2913 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2963 TCGA-AB-2967 
       38.99        39.98         1.02         2.96        53.98        34.03 
TCGA-AB-2970 TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2976 TCGA-AB-2985 TCGA-AB-2986 
       10.03         0.99        20.02        30.08         8.98         6.97 
TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2993 TCGA-AB-3006 
        0.99        12.00        25.02        15.95 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.00     0.00     0.00     0.99     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   69.04    84.07    56.09    94.06    55.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   6.970   21.980   10.535   20.545    8.980 
[1] "0.0 - 69.0 (7.0)"  "0.0 - 84.1 (22.0)" "0.0 - 56.1 (10.5)"
[4] "1.0 - 94.1 (20.5)" "0.0 - 55.0 (9.0)" 
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 12 13
  subtype2 13 12
  subtype3 26 36
  subtype4 16 22
  subtype5 22 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   13
  subtype2   13   12
  subtype3   26   36
  subtype4   16   22
  subtype5   22   22
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       12       13       26       16       22
  MALE         13       12       36       22       22
[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     0                         0    25
  subtype2     0                         3    21
  subtype3     0                         4    58
  subtype4     1                         1    35
  subtype5     1                         5    38
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        1        1
  BLACK OR AFRICAN AMERICAN        0        3        4        1        5
  WHITE                           25       21       58       35       38
[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 25
  subtype2  0 24
  subtype3  0 61
  subtype4  1 36
  subtype5  0 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   25
  subtype2    0   24
  subtype3    0   61
  subtype4    1   36
  subtype5    0   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        0        1        0
  NOT HISPANIC OR LATINO       25       24       61       36       44
[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 43
  subtype2 17 33
  subtype3 14 27
subtype1 subtype2 subtype3 
      69       50       41 
subtype1 subtype2 subtype3 
      43       33       27 
$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-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2830 TCGA-AB-2838 
       82.06         0.00        27.02        31.99         9.04        12.00 
TCGA-AB-2843 TCGA-AB-2845 TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2854 TCGA-AB-2857 
        7.07         9.99        19.99        72.99        12.03        10.06 
TCGA-AB-2858 TCGA-AB-2860 TCGA-AB-2863 TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 
       18.97        14.04         1.02         2.01         6.05         4.96 
TCGA-AB-2872 TCGA-AB-2875 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2890 
       20.98         6.97        12.00         7.04         5.95         0.00 
TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 
       12.92        22.06         1.94        17.00         1.02         0.99 
TCGA-AB-2917 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 
       39.98         2.96         4.04         2.01         1.94         7.07 
TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 
        9.99        14.96         0.00        22.98        10.06         1.02 
TCGA-AB-2955 TCGA-AB-2959 TCGA-AB-2964 TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2978 
       16.08        16.08        41.98        28.08        10.03        22.98 
TCGA-AB-2979 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2991 TCGA-AB-2992 
       22.06        22.98         4.93        11.01        60.03        56.09 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       50.99        51.98        57.04        41.06        51.98        47.05 
TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3012 
       27.02        18.97        62.04 

$subtype2
TCGA-AB-2805 TCGA-AB-2813 TCGA-AB-2815 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2824 
       18.97         1.02        27.02         8.05         9.96         0.99 
TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2828 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 
        6.97        24.03        75.09        14.99         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2846 TCGA-AB-2851 
       17.03         0.00         0.00         4.01        46.09         7.96 
TCGA-AB-2856 TCGA-AB-2861 TCGA-AB-2866 TCGA-AB-2870 TCGA-AB-2873 TCGA-AB-2881 
        4.93         0.00         5.03         5.03         8.98        12.92 
TCGA-AB-2884 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2900 TCGA-AB-2910 TCGA-AB-2911 
       24.03        10.98         9.99         6.05         0.00        38.99 
TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 TCGA-AB-2924 TCGA-AB-2925 
        9.01        26.04         0.00        29.00         2.96         7.99 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2942 TCGA-AB-2948 TCGA-AB-2954 TCGA-AB-2956 
        4.01         0.92        21.07        19.07        49.05         6.02 
TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2973 TCGA-AB-2981 TCGA-AB-2985 
       11.01        34.03        37.05        20.02        16.01         8.98 
TCGA-AB-2987 TCGA-AB-3005 
        6.05        69.04 

$subtype3
TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2812 TCGA-AB-2823 TCGA-AB-2832 TCGA-AB-2839 
        1.02         7.99        12.03         0.00        12.00        15.98 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2848 TCGA-AB-2853 TCGA-AB-2855 TCGA-AB-2859 
        0.92        46.06        14.96         2.93         6.97         9.99 
TCGA-AB-2862 TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2874 TCGA-AB-2877 TCGA-AB-2879 
       47.01         7.99         5.03        13.02        20.98         8.05 
TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2903 TCGA-AB-2913 TCGA-AB-2919 
        5.03         7.04         7.99         0.00        39.98         2.01 
TCGA-AB-2920 TCGA-AB-2931 TCGA-AB-2963 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2976 
       12.03         0.00        53.98        26.04         0.99        30.08 
TCGA-AB-2977 TCGA-AB-2984 TCGA-AB-2986 TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2993 
        1.02        38.04         6.97         0.99        15.02        25.02 
TCGA-AB-2994 TCGA-AB-2998 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3011 
       59.11         1.02        15.95        51.98        61.97 

subtype1 subtype2 subtype3 
       0        0        0 
subtype1 subtype2 subtype3 
   94.06    75.09    61.97 
subtype1 subtype2 subtype3 
  14.040    9.485    9.990 
[1] "0.0 - 94.1 (14.0)" "0.0 - 75.1 (9.5)"  "0.0 - 62.0 (10.0)"
D3V2, continuous
D3V3, binary
          cls
clus        0  1
  subtype1 32 43
  subtype2 21 31
  subtype3 27 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   43
  subtype2   21   31
  subtype3   27   19
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       21       27
  MALE         43       31       19
[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    69
  subtype2     1                         2    49
  subtype3     0                         8    38
D3V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        0
  BLACK OR AFRICAN AMERICAN        3        2        8
  WHITE                           69       49       38
[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 72
  subtype2  1 51
  subtype3  0 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   72
  subtype2    1   51
  subtype3    0   46
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        0
  NOT HISPANIC OR LATINO       72       51       46
[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  5
  subtype2  9  5
  subtype3  7  5
  subtype4 12 41
  subtype5 10 15
  subtype6  8 32
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      16       14       12       53       25       40 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       5        5        5       41       15       32 
$subtype1
TCGA-AB-2803 TCGA-AB-2823 TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2862 TCGA-AB-2872 
       26.04         0.00         0.92        46.06        47.01        20.98 
TCGA-AB-2897 TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2991 TCGA-AB-2994 TCGA-AB-2998 
        7.99        22.98         4.93        60.03        59.11         1.02 
TCGA-AB-2999 TCGA-AB-3001 TCGA-AB-3007 TCGA-AB-3012 
       57.04        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-2886 TCGA-AB-2937 TCGA-AB-2950 TCGA-AB-2979 TCGA-AB-3000 TCGA-AB-3008 
        5.95         7.07        10.06        22.06        41.06        27.02 

$subtype4
TCGA-AB-2807 TCGA-AB-2814 TCGA-AB-2817 TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 
        5.95        26.04         8.98         0.00        27.02        31.99 
TCGA-AB-2830 TCGA-AB-2838 TCGA-AB-2843 TCGA-AB-2847 TCGA-AB-2849 TCGA-AB-2854 
        9.04        12.00         7.07        19.99        72.99        12.03 
TCGA-AB-2855 TCGA-AB-2857 TCGA-AB-2860 TCGA-AB-2863 TCGA-AB-2865 TCGA-AB-2867 
        6.97        10.06        14.04         1.02         2.01         6.05 
TCGA-AB-2868 TCGA-AB-2874 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2890 TCGA-AB-2898 
        4.96        13.02        12.00         7.04         0.00        12.92 
TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2912 
       22.06         1.94        17.00         1.02         0.99         9.01 
TCGA-AB-2915 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2933 
        0.00        39.98        12.03         2.96         4.04         4.01 
TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2938 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2949 
        2.01         1.94         9.99        14.96         0.00        22.98 
TCGA-AB-2952 TCGA-AB-2955 TCGA-AB-2959 TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2978 
        1.02        16.08        16.08        28.08        10.03        22.98 
TCGA-AB-2983 TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-3002 TCGA-AB-3009 
       11.01        50.99        51.98        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-2903 
        5.03        20.98         8.05         5.03         7.04         0.00 
TCGA-AB-2913 TCGA-AB-2919 TCGA-AB-2931 TCGA-AB-2964 TCGA-AB-2972 TCGA-AB-2976 
       39.98         2.01         0.00        41.98         0.99        30.08 
TCGA-AB-2984 TCGA-AB-2986 TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2993 TCGA-AB-3006 
       38.04         6.97         0.99        15.02        25.02        15.95 
TCGA-AB-3011 
       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-2837 
       24.03        12.00         8.05        55.00        17.03         0.00 
TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2856 TCGA-AB-2861 
        0.00         4.01        14.96         7.96         4.93         0.00 
TCGA-AB-2866 TCGA-AB-2873 TCGA-AB-2884 TCGA-AB-2900 TCGA-AB-2910 TCGA-AB-2911 
        5.03         8.98        24.03         6.05         0.00        38.99 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2948 TCGA-AB-2956 TCGA-AB-2963 TCGA-AB-2965 
        2.96         7.99        19.07         6.02        53.98        11.01 
TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2973 TCGA-AB-2977 TCGA-AB-2981 
       34.03        37.05        26.04        20.02         1.02        16.01 
TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-2992 TCGA-AB-3005 
        8.98         6.05        56.09        69.04 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.00     0.92     5.95     0.00     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   62.04    75.09    94.06    72.99    61.97    69.04 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  36.050   20.020   20.515   10.060    8.050    8.515 
[1] "0.0 - 62.0 (36.0)" "0.9 - 75.1 (20.0)" "6.0 - 94.1 (20.5)"
[4] "0.0 - 73.0 (10.1)" "0.0 - 62.0 (8.1)"  "0.0 - 69.0 (8.5)" 
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 16 42
  subtype2 15 15
  subtype3 18 19
  subtype4  9 21
  subtype5  4 15
subtype1 subtype2 subtype3 subtype4 subtype5 
      58       30       37       30       19 
subtype1 subtype2 subtype3 subtype4 subtype5 
      42       15       19       21       15 
$subtype1
TCGA-AB-2802 TCGA-AB-2810 TCGA-AB-2811 TCGA-AB-2816 TCGA-AB-2818 TCGA-AB-2824 
       12.00         1.02         7.99         8.05         9.96         0.99 
TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2834 TCGA-AB-2835 
        6.97        24.03        12.00        14.99         8.05        55.00 
TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2842 TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2853 
       17.03         0.00         0.00        14.96         7.96         2.93 
TCGA-AB-2855 TCGA-AB-2856 TCGA-AB-2861 TCGA-AB-2866 TCGA-AB-2873 TCGA-AB-2877 
        6.97         4.93         0.00         5.03         8.98        20.98 
TCGA-AB-2879 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2896 
        8.05        24.00        24.03         6.97         5.95         7.04 
TCGA-AB-2900 TCGA-AB-2903 TCGA-AB-2911 TCGA-AB-2916 TCGA-AB-2923 TCGA-AB-2924 
        6.05         0.00        38.99        29.00         1.02         2.96 
TCGA-AB-2925 TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2945 TCGA-AB-2947 
        7.99         0.00         4.01         0.92         7.99         1.02 
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-2973 TCGA-AB-2976 TCGA-AB-2981 TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-2988 
       20.02        30.08        16.01         8.98         6.05         0.99 
TCGA-AB-2989 TCGA-AB-2990 TCGA-AB-3005 TCGA-AB-3011 
       12.00        15.02        69.04        61.97 

$subtype2
TCGA-AB-2803 TCGA-AB-2821 TCGA-AB-2823 TCGA-AB-2838 TCGA-AB-2840 TCGA-AB-2841 
       26.04        27.02         0.00        12.00         0.92        46.06 
TCGA-AB-2857 TCGA-AB-2865 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2872 TCGA-AB-2878 
       10.06         2.01         6.05         4.96        20.98        12.00 
TCGA-AB-2885 TCGA-AB-2888 TCGA-AB-2897 TCGA-AB-2917 TCGA-AB-2929 TCGA-AB-2935 
        7.04        10.98         7.99        39.98         4.04         2.01 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2949 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2991 
       14.96         0.00        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-2812 TCGA-AB-2814 TCGA-AB-2819 TCGA-AB-2822 
       18.97        31.07        12.03        26.04        82.06        31.99 
TCGA-AB-2839 TCGA-AB-2844 TCGA-AB-2849 TCGA-AB-2858 TCGA-AB-2863 TCGA-AB-2874 
       15.98         4.01        72.99        18.97         1.02        13.02 
TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2881 TCGA-AB-2886 TCGA-AB-2889 TCGA-AB-2895 
        6.97        40.08        12.92         5.95         9.99         5.03 
TCGA-AB-2909 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2919 TCGA-AB-2920 TCGA-AB-2926 
        0.99        39.98        26.04         2.01        12.03        15.02 
TCGA-AB-2937 TCGA-AB-2942 TCGA-AB-2955 TCGA-AB-2957 TCGA-AB-2964 TCGA-AB-2966 
        7.07        21.07        16.08        20.02        41.98        28.08 
TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2984 TCGA-AB-2986 TCGA-AB-2993 TCGA-AB-3000 
        1.02        22.06        38.04         6.97        25.02        41.06 
TCGA-AB-3009 
       18.97 

$subtype4
TCGA-AB-2807 TCGA-AB-2808 TCGA-AB-2813 TCGA-AB-2815 TCGA-AB-2817 TCGA-AB-2828 
        5.95        94.06         1.02        27.02         8.98        75.09 
TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2854 TCGA-AB-2862 TCGA-AB-2870 TCGA-AB-2882 
        9.99        46.09        12.03        47.01         5.03        12.00 
TCGA-AB-2892 TCGA-AB-2898 TCGA-AB-2901 TCGA-AB-2910 TCGA-AB-2912 TCGA-AB-2915 
       31.00        12.92         1.94         0.00         9.01         0.00 
TCGA-AB-2922 TCGA-AB-2927 TCGA-AB-2938 TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2954 
        0.00         2.96         9.99        19.07        10.06        49.05 
TCGA-AB-2970 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2998 TCGA-AB-3002 TCGA-AB-3008 
       10.03         4.93        11.01         1.02        47.05        27.02 

$subtype5
TCGA-AB-2820 TCGA-AB-2830 TCGA-AB-2843 TCGA-AB-2847 TCGA-AB-2859 TCGA-AB-2860 
        0.00         9.04         7.07        19.99         9.99        14.04 
TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2890 TCGA-AB-2899 TCGA-AB-2904 TCGA-AB-2908 
        7.99         5.03         0.00        22.06        17.00         1.02 
TCGA-AB-2936 TCGA-AB-2952 TCGA-AB-2959 TCGA-AB-2972 TCGA-AB-2992 TCGA-AB-2996 
        1.94         1.02        16.08         0.99        56.09        51.98 
TCGA-AB-3006 
       15.95 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.00     0.00     0.99     0.00     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   69.04    62.04    82.06    94.06    56.09 
subtype1 subtype2 subtype3 subtype4 subtype5 
   8.050   17.970   18.970   10.045    9.040 
[1] "0.0 - 69.0 (8.1)"  "0.0 - 62.0 (18.0)" "1.0 - 82.1 (19.0)"
[4] "0.0 - 94.1 (10.0)" "0.0 - 56.1 (9.0)" 
D5V2, continuous
D5V3, binary
          cls
clus        0  1
  subtype1 26 34
  subtype2 12 19
  subtype3 22 21
  subtype4 17 16
  subtype5 10 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   34
  subtype2   12   19
  subtype3   22   21
  subtype4   17   16
  subtype5   10   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       26       12       22       17       10
  MALE         34       19       21       16       11
[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                         3    56
  subtype2     0                         1    30
  subtype3     1                         4    37
  subtype4     0                         2    30
  subtype5     0                         3    18
D5V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        0        0
  BLACK OR AFRICAN AMERICAN        3        1        4        2        3
  WHITE                           56       30       37       30       18
[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"
D5V5, binary
          cls
clus        0  1
  subtype1  1 59
  subtype2  0 31
  subtype3  0 42
  subtype4  0 31
  subtype5  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   59
  subtype2    0   31
  subtype3    0   42
  subtype4    0   31
  subtype5    0   21
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        0        0        0        0
  NOT HISPANIC OR LATINO       59       31       42       31       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(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 20 48
  subtype2 14 19
  subtype3 28 45
subtype1 subtype2 subtype3 
      68       33       73 
subtype1 subtype2 subtype3 
      48       19       45 
$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-2837 TCGA-AB-2839 TCGA-AB-2842 TCGA-AB-2848 TCGA-AB-2851 
       17.03         0.00        15.98         0.00        14.96         7.96 
TCGA-AB-2853 TCGA-AB-2856 TCGA-AB-2861 TCGA-AB-2866 TCGA-AB-2869 TCGA-AB-2871 
        2.93         4.93         0.00         5.03         7.99         5.03 
TCGA-AB-2873 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 
        8.98        20.98         8.05        24.00        24.03         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2900 TCGA-AB-2903 TCGA-AB-2910 
        5.95         5.03         7.04         6.05         0.00         0.00 
TCGA-AB-2911 TCGA-AB-2913 TCGA-AB-2919 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
       38.99        39.98         2.01         1.02         2.96         7.99 
TCGA-AB-2931 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2956 TCGA-AB-2963 TCGA-AB-2964 
        0.00         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-2820 TCGA-AB-2821 TCGA-AB-2823 TCGA-AB-2838 
       26.04        26.04         0.00        27.02         0.00        12.00 
TCGA-AB-2840 TCGA-AB-2841 TCGA-AB-2843 TCGA-AB-2857 TCGA-AB-2859 TCGA-AB-2865 
        0.92        46.06         7.07        10.06         9.99         2.01 
TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2872 TCGA-AB-2878 TCGA-AB-2885 TCGA-AB-2888 
        6.05         4.96        20.98        12.00         7.04        10.98 
TCGA-AB-2897 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2949 
        7.99         4.04         2.01        14.96         0.00        22.98 
TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2991 TCGA-AB-2994 TCGA-AB-2995 TCGA-AB-2999 
       22.98        22.98        60.03        59.11        50.99        57.04 
TCGA-AB-3001 TCGA-AB-3007 TCGA-AB-3012 
       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-2881 TCGA-AB-2882 TCGA-AB-2886 
       13.02         6.97        40.08        12.92        12.00         5.95 
TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 
        9.99         0.00        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-2915 
       17.00         1.02         0.99         9.01        26.04         0.00 
TCGA-AB-2916 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2926 TCGA-AB-2927 
       29.00        39.98        12.03         0.00        15.02         2.96 
TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 TCGA-AB-2942 
        4.01         0.92         1.94         7.07         9.99        21.07 
TCGA-AB-2948 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2957 
       19.07        10.06         1.02        49.05        16.08        20.02 
TCGA-AB-2959 TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2982 
       16.08        28.08        10.03         1.02        22.06         4.93 
TCGA-AB-2983 TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-3000 TCGA-AB-3002 TCGA-AB-3008 
       11.01        51.98         1.02        41.06        47.05        27.02 
TCGA-AB-3009 
       18.97 

subtype1 subtype2 subtype3 
       0        0        0 
subtype1 subtype2 subtype3 
   69.04    62.04    94.06 
subtype1 subtype2 subtype3 
    8.05    12.00    12.92 
[1] "0.0 - 69.0 (8.1)"  "0.0 - 62.0 (12.0)" "0.0 - 94.1 (12.9)"
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"
