[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/19775300/LAML-TB.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LAML-TB/19785823/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 
148  14  27   2 
  1   2   3 
148  14  27 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
34 63 50 47 
 1  2  3  4 
34 63 50 47 
[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] "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 54 85
  subtype2  3  9
  subtype3  4 21
subtype1 subtype2 subtype3 
     139       12       25 
subtype1 subtype2 subtype3 
      85        9       21 
$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-2823 TCGA-AB-2824 
        9.96        82.06        27.02        31.99         0.00         0.99 
TCGA-AB-2825 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2828 TCGA-AB-2831 TCGA-AB-2832 
        6.97        24.03         8.98        75.09        21.04        12.00 
TCGA-AB-2834 TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2839 TCGA-AB-2840 
        8.05        55.00        17.03         0.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2845 TCGA-AB-2846 TCGA-AB-2848 
       46.06         0.00         4.01         9.99        46.09        14.96 
TCGA-AB-2850 TCGA-AB-2851 TCGA-AB-2853 TCGA-AB-2854 TCGA-AB-2856 TCGA-AB-2858 
        2.01         7.96         2.93        12.03         4.93        18.97 
TCGA-AB-2859 TCGA-AB-2861 TCGA-AB-2862 TCGA-AB-2863 TCGA-AB-2864 TCGA-AB-2867 
        9.99         0.00        47.01         1.02        18.97         6.05 
TCGA-AB-2869 TCGA-AB-2870 TCGA-AB-2871 TCGA-AB-2872 TCGA-AB-2873 TCGA-AB-2874 
        7.99         5.03         5.03        20.98         8.98        13.02 
TCGA-AB-2875 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2881 TCGA-AB-2882 TCGA-AB-2884 
        6.97        20.98         8.05        12.92        12.00        24.03 
TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2890 TCGA-AB-2892 TCGA-AB-2893 
        5.95        10.98         9.99         0.00        31.00         6.97 
TCGA-AB-2894 TCGA-AB-2895 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2898 TCGA-AB-2899 
        5.95         5.03         7.04         7.99        12.92        22.06 
TCGA-AB-2900 TCGA-AB-2903 TCGA-AB-2905 TCGA-AB-2906 TCGA-AB-2909 TCGA-AB-2910 
        6.05         0.00        52.96        18.97         0.99         0.00 
TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2913 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2919 
       38.99         9.01        39.98        26.04         0.00         2.01 
TCGA-AB-2922 TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2926 TCGA-AB-2927 TCGA-AB-2931 
        0.00         2.96         7.99        15.02         2.96         0.00 
TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2942 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2949 
        1.94         7.07        21.07         7.99         1.02        22.98 
TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2957 TCGA-AB-2959 TCGA-AB-2963 
       10.06        49.05         6.02        20.02        16.08        53.98 
TCGA-AB-2965 TCGA-AB-2966 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2972 
       11.01        28.08        34.03        37.05        26.04         0.99 
TCGA-AB-2973 TCGA-AB-2974 TCGA-AB-2976 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2982 
       20.02         3.02        30.08        22.98        22.98         4.93 
TCGA-AB-2984 TCGA-AB-2985 TCGA-AB-2986 TCGA-AB-2987 TCGA-AB-2988 TCGA-AB-2989 
       38.04         8.98         6.97         6.05         0.99        12.00 
TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2993 TCGA-AB-2994 TCGA-AB-2995 
       15.02        60.03        56.09        25.02        59.11        50.99 
TCGA-AB-2996 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 
       51.98         1.02        57.04        41.06        51.98        47.05 
TCGA-AB-3005 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3008 TCGA-AB-3009 TCGA-AB-3011 
       69.04        15.95        51.98        27.02        18.97        61.97 
TCGA-AB-3012 
       62.04 

$subtype2
TCGA-AB-2805 TCGA-AB-2820 TCGA-AB-2830 TCGA-AB-2866 TCGA-AB-2916 TCGA-AB-2923 
       18.97         0.00         9.04         5.03        29.00         1.02 
TCGA-AB-2934 TCGA-AB-2948 TCGA-AB-2964 TCGA-AB-2970 TCGA-AB-2977 TCGA-AB-2983 
        0.92        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-2941 TCGA-AB-2952 TCGA-AB-2955 
        4.01         2.01         9.99         0.00         1.02        16.08 
TCGA-AB-2968 
       15.06 

subtype1 subtype2 subtype3 
       0        0        0 
subtype1 subtype2 subtype3 
   94.06    41.98    72.99 
subtype1 subtype2 subtype3 
  12.030    9.535    8.980 
[1] "0.0 - 94.1 (12.0)" "0.0 - 42.0 (9.5)"  "0.0 - 73.0 (9.0)" 
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 73 75
  subtype2  6  8
  subtype3  7 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73   75
  subtype2    6    8
  subtype3    7   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       73        6        7
  MALE         75        8       20
[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     2                        11   133
  subtype2     0                         1    13
  subtype3     0                         2    25
D1V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN       11        1        2
  WHITE                          133       13       25
[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"
D1V5, binary
          cls
clus         0   1
  subtype1   2 143
  subtype2   1  13
  subtype3   0  27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  143
  subtype2    1   13
  subtype3    0   27
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO      143       13       27
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 20 12
  subtype2 11 46
  subtype3 20 28
  subtype4 12 30
subtype1 subtype2 subtype3 subtype4 
      32       57       48       42 
subtype1 subtype2 subtype3 subtype4 
      12       46       28       30 
$subtype1
TCGA-AB-2802 TCGA-AB-2803 TCGA-AB-2804 TCGA-AB-2816 TCGA-AB-2823 TCGA-AB-2840 
       12.00        26.04        84.07         8.05         0.00         0.92 
TCGA-AB-2841 TCGA-AB-2845 TCGA-AB-2862 TCGA-AB-2872 TCGA-AB-2881 TCGA-AB-2884 
       46.06         9.99        47.01        20.98        12.92        24.03 
TCGA-AB-2892 TCGA-AB-2893 TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2906 TCGA-AB-2919 
       31.00         6.97         7.04         7.99        18.97         2.01 
TCGA-AB-2942 TCGA-AB-2957 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2980 TCGA-AB-2982 
       21.07        20.02        37.05        26.04        22.98         4.93 
TCGA-AB-2984 TCGA-AB-2990 TCGA-AB-2991 TCGA-AB-2998 TCGA-AB-2999 TCGA-AB-3007 
       38.04        15.02        60.03         1.02        57.04        51.98 
TCGA-AB-3011 TCGA-AB-3012 
       61.97        62.04 

$subtype2
TCGA-AB-2805 TCGA-AB-2807 TCGA-AB-2810 TCGA-AB-2813 TCGA-AB-2814 TCGA-AB-2817 
       18.97         5.95         1.02         1.02        26.04         8.98 
TCGA-AB-2820 TCGA-AB-2821 TCGA-AB-2822 TCGA-AB-2829 TCGA-AB-2830 TCGA-AB-2831 
        0.00        27.02        31.99         8.98         9.04        21.04 
TCGA-AB-2838 TCGA-AB-2843 TCGA-AB-2847 TCGA-AB-2854 TCGA-AB-2857 TCGA-AB-2860 
       12.00         7.07        19.99        12.03        10.06        14.04 
TCGA-AB-2863 TCGA-AB-2867 TCGA-AB-2868 TCGA-AB-2873 TCGA-AB-2878 TCGA-AB-2882 
        1.02         6.05         4.96         8.98        12.00        12.00 
TCGA-AB-2885 TCGA-AB-2890 TCGA-AB-2898 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 
        7.04         0.00        12.92        22.06         1.94        17.00 
TCGA-AB-2908 TCGA-AB-2915 TCGA-AB-2917 TCGA-AB-2920 TCGA-AB-2922 TCGA-AB-2926 
        1.02         0.00        39.98        12.03         0.00        15.02 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2935 TCGA-AB-2936 
        2.96         4.04         4.01         0.92         2.01         1.94 
TCGA-AB-2938 TCGA-AB-2941 TCGA-AB-2948 TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-2959 
        9.99         0.00        19.07        22.98         1.02        16.08 
TCGA-AB-2964 TCGA-AB-2968 TCGA-AB-2978 TCGA-AB-2983 TCGA-AB-2987 TCGA-AB-2992 
       41.98        15.06        22.98        11.01         6.05        56.09 
TCGA-AB-2995 TCGA-AB-2996 TCGA-AB-3002 
       50.99        51.98        47.05 

$subtype3
TCGA-AB-2806 TCGA-AB-2808 TCGA-AB-2809 TCGA-AB-2811 TCGA-AB-2815 TCGA-AB-2819 
       31.07        94.06         2.04         7.99        27.02        82.06 
TCGA-AB-2825 TCGA-AB-2828 TCGA-AB-2832 TCGA-AB-2833 TCGA-AB-2839 TCGA-AB-2846 
        6.97        75.09        12.00        14.99        15.98        46.09 
TCGA-AB-2849 TCGA-AB-2853 TCGA-AB-2855 TCGA-AB-2858 TCGA-AB-2861 TCGA-AB-2870 
       72.99         2.93         6.97        18.97         0.00         5.03 
TCGA-AB-2875 TCGA-AB-2883 TCGA-AB-2886 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2894 
        6.97        24.00         5.95        10.98         9.99         5.95 
TCGA-AB-2895 TCGA-AB-2909 TCGA-AB-2910 TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2916 
        5.03         0.99         0.00         9.01        26.04        29.00 
TCGA-AB-2925 TCGA-AB-2931 TCGA-AB-2937 TCGA-AB-2939 TCGA-AB-2945 TCGA-AB-2947 
        7.99         0.00         7.07        14.96         7.99         1.02 
TCGA-AB-2950 TCGA-AB-2954 TCGA-AB-2955 TCGA-AB-2956 TCGA-AB-2965 TCGA-AB-2966 
       10.06        49.05        16.08         6.02        11.01        28.08 
TCGA-AB-2974 TCGA-AB-2981 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3005 TCGA-AB-3009 
        3.02        16.01        41.06        51.98        69.04        18.97 

$subtype4
TCGA-AB-2812 TCGA-AB-2818 TCGA-AB-2824 TCGA-AB-2826 TCGA-AB-2827 TCGA-AB-2834 
       12.03         9.96         0.99        24.03         8.98         8.05 
TCGA-AB-2835 TCGA-AB-2836 TCGA-AB-2837 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2848 
       55.00        17.03         0.00         0.00         4.01        14.96 
TCGA-AB-2851 TCGA-AB-2856 TCGA-AB-2866 TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2874 
        7.96         4.93         5.03         7.99         5.03        13.02 
TCGA-AB-2876 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2900 TCGA-AB-2903 TCGA-AB-2911 
       40.08        20.98         8.05         6.05         0.00        38.99 
TCGA-AB-2913 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2963 TCGA-AB-2967 TCGA-AB-2970 
       39.98         1.02         2.96        53.98        34.03        10.03 
TCGA-AB-2972 TCGA-AB-2973 TCGA-AB-2976 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2985 
        0.99        20.02        30.08         1.02        22.06         8.98 
TCGA-AB-2986 TCGA-AB-2988 TCGA-AB-2989 TCGA-AB-2993 TCGA-AB-3006 TCGA-AB-3008 
        6.97         0.99        12.00        25.02        15.95        27.02 

subtype1 subtype2 subtype3 subtype4 
       0        0        0        0 
subtype1 subtype2 subtype3 subtype4 
   84.07    56.09    94.06    55.00 
subtype1 subtype2 subtype3 subtype4 
  21.025   10.060   10.995    9.470 
[1] "0.0 - 84.1 (21.0)" "0.0 - 56.1 (10.1)" "0.0 - 94.1 (11.0)"
[4] "0.0 - 55.0 (9.5)" 
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 19 15
  subtype2 26 37
  subtype3 21 29
  subtype4 23 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   15
  subtype2   26   37
  subtype3   21   29
  subtype4   23   24
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       19       26       21       23
  MALE         15       37       29       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     0                         2    31
  subtype2     0                         5    58
  subtype3     1                         1    47
  subtype4     1                         5    41
D2V4, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        0        1        1
  BLACK OR AFRICAN AMERICAN        2        5        1        5
  WHITE                           31       58       47       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"
D2V5, binary
          cls
clus        0  1
  subtype1  0 33
  subtype2  0 62
  subtype3  1 48
  subtype4  0 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   33
  subtype2    0   62
  subtype3    1   48
  subtype4    0   47
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        0        1        0
  NOT HISPANIC OR LATINO       33       62       48       47
[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(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 26 42
  subtype2 17 35
  subtype3 14 26
subtype1 subtype2 subtype3 
      68       52       40 
subtype1 subtype2 subtype3 
      42       35       26 
$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-2868 TCGA-AB-2872 
       18.97        14.04         1.02         2.01         4.96        20.98 
TCGA-AB-2875 TCGA-AB-2882 TCGA-AB-2885 TCGA-AB-2886 TCGA-AB-2890 TCGA-AB-2898 
        6.97        12.00         7.04         5.95         0.00        12.92 
TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2904 TCGA-AB-2908 TCGA-AB-2909 TCGA-AB-2917 
       22.06         1.94        17.00         1.02         0.99        39.98 
TCGA-AB-2927 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2936 TCGA-AB-2937 TCGA-AB-2938 
        2.96         4.04         2.01         1.94         7.07         9.99 
TCGA-AB-2939 TCGA-AB-2941 TCGA-AB-2949 TCGA-AB-2950 TCGA-AB-2952 TCGA-AB-2955 
       14.96         0.00        22.98        10.06         1.02        16.08 
TCGA-AB-2959 TCGA-AB-2964 TCGA-AB-2966 TCGA-AB-2970 TCGA-AB-2978 TCGA-AB-2979 
       16.08        41.98        28.08        10.03        22.98        22.06 
TCGA-AB-2980 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2991 TCGA-AB-2992 TCGA-AB-2995 
       22.98         4.93        11.01        60.03        56.09        50.99 
TCGA-AB-2996 TCGA-AB-2999 TCGA-AB-3000 TCGA-AB-3001 TCGA-AB-3002 TCGA-AB-3008 
       51.98        57.04        41.06        51.98        47.05        27.02 
TCGA-AB-3009 TCGA-AB-3012 
       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-2837 TCGA-AB-2842 TCGA-AB-2844 TCGA-AB-2846 
       55.00        17.03         0.00         0.00         4.01        46.09 
TCGA-AB-2851 TCGA-AB-2856 TCGA-AB-2861 TCGA-AB-2866 TCGA-AB-2867 TCGA-AB-2870 
        7.96         4.93         0.00         5.03         6.05         5.03 
TCGA-AB-2873 TCGA-AB-2881 TCGA-AB-2884 TCGA-AB-2888 TCGA-AB-2889 TCGA-AB-2900 
        8.98        12.92        24.03        10.98         9.99         6.05 
TCGA-AB-2910 TCGA-AB-2911 TCGA-AB-2912 TCGA-AB-2914 TCGA-AB-2915 TCGA-AB-2916 
        0.00        38.99         9.01        26.04         0.00        29.00 
TCGA-AB-2924 TCGA-AB-2925 TCGA-AB-2933 TCGA-AB-2934 TCGA-AB-2942 TCGA-AB-2948 
        2.96         7.99         4.01         0.92        21.07        19.07 
TCGA-AB-2954 TCGA-AB-2956 TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2973 
       49.05         6.02        11.01        34.03        37.05        20.02 
TCGA-AB-2981 TCGA-AB-2985 TCGA-AB-2987 TCGA-AB-3005 
       16.01         8.98         6.05        69.04 

$subtype3
TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2823 TCGA-AB-2832 TCGA-AB-2839 TCGA-AB-2840 
        1.02        12.03         0.00        12.00        15.98         0.92 
TCGA-AB-2841 TCGA-AB-2848 TCGA-AB-2853 TCGA-AB-2855 TCGA-AB-2859 TCGA-AB-2862 
       46.06        14.96         2.93         6.97         9.99        47.01 
TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2874 TCGA-AB-2877 TCGA-AB-2879 TCGA-AB-2895 
        7.99         5.03        13.02        20.98         8.05         5.03 
TCGA-AB-2896 TCGA-AB-2897 TCGA-AB-2903 TCGA-AB-2913 TCGA-AB-2919 TCGA-AB-2920 
        7.04         7.99         0.00        39.98         2.01        12.03 
TCGA-AB-2931 TCGA-AB-2963 TCGA-AB-2971 TCGA-AB-2972 TCGA-AB-2976 TCGA-AB-2977 
        0.00        53.98        26.04         0.99        30.08         1.02 
TCGA-AB-2984 TCGA-AB-2986 TCGA-AB-2988 TCGA-AB-2990 TCGA-AB-2993 TCGA-AB-2994 
       38.04         6.97         0.99        15.02        25.02        59.11 
TCGA-AB-2998 TCGA-AB-3006 TCGA-AB-3007 TCGA-AB-3011 
        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 
  14.500    8.995   10.995 
[1] "0.0 - 94.1 (14.5)" "0.0 - 75.1 (9.0)"  "0.0 - 62.0 (11.0)"
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  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 15 43
  subtype2 16 20
  subtype3 12 27
  subtype4 19 22
subtype1 subtype2 subtype3 subtype4 
      58       36       39       41 
subtype1 subtype2 subtype3 subtype4 
      43       20       27       22 
$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-2837 TCGA-AB-2842 TCGA-AB-2848 TCGA-AB-2851 TCGA-AB-2855 TCGA-AB-2856 
        0.00         0.00        14.96         7.96         6.97         4.93 
TCGA-AB-2861 TCGA-AB-2866 TCGA-AB-2869 TCGA-AB-2871 TCGA-AB-2873 TCGA-AB-2877 
        0.00         5.03         7.99         5.03         8.98        20.98 
TCGA-AB-2883 TCGA-AB-2884 TCGA-AB-2893 TCGA-AB-2894 TCGA-AB-2896 TCGA-AB-2900 
       24.00        24.03         6.97         5.95         7.04         6.05 
TCGA-AB-2903 TCGA-AB-2911 TCGA-AB-2916 TCGA-AB-2923 TCGA-AB-2924 TCGA-AB-2925 
        0.00        38.99        29.00         1.02         2.96         7.99 
TCGA-AB-2931 TCGA-AB-2933 TCGA-AB-2945 TCGA-AB-2947 TCGA-AB-2948 TCGA-AB-2956 
        0.00         4.01         7.99         1.02        19.07         6.02 
TCGA-AB-2963 TCGA-AB-2965 TCGA-AB-2967 TCGA-AB-2969 TCGA-AB-2971 TCGA-AB-2972 
       53.98        11.01        34.03        37.05        26.04         0.99 
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-3006 
       12.00        15.02        69.04        15.95 

$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-2843 TCGA-AB-2857 TCGA-AB-2859 TCGA-AB-2860 TCGA-AB-2865 TCGA-AB-2867 
        7.07        10.06         9.99        14.04         2.01         6.05 
TCGA-AB-2868 TCGA-AB-2872 TCGA-AB-2878 TCGA-AB-2885 TCGA-AB-2888 TCGA-AB-2897 
        4.96        20.98        12.00         7.04        10.98         7.99 
TCGA-AB-2898 TCGA-AB-2917 TCGA-AB-2929 TCGA-AB-2935 TCGA-AB-2939 TCGA-AB-2941 
       12.92        39.98         4.04         2.01        14.96         0.00 
TCGA-AB-2949 TCGA-AB-2952 TCGA-AB-2978 TCGA-AB-2980 TCGA-AB-2991 TCGA-AB-2992 
       22.98         1.02        22.98        22.98        60.03        56.09 
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-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-2890 
       12.03        47.01         5.03        12.92        12.00         0.00 
TCGA-AB-2892 TCGA-AB-2899 TCGA-AB-2901 TCGA-AB-2908 TCGA-AB-2910 TCGA-AB-2912 
       31.00        22.06         1.94         1.02         0.00         9.01 
TCGA-AB-2915 TCGA-AB-2922 TCGA-AB-2927 TCGA-AB-2936 TCGA-AB-2938 TCGA-AB-2950 
        0.00         0.00         2.96         1.94         9.99        10.06 
TCGA-AB-2954 TCGA-AB-2959 TCGA-AB-2970 TCGA-AB-2982 TCGA-AB-2983 TCGA-AB-2996 
       49.05        16.08        10.03         4.93        11.01        51.98 
TCGA-AB-2998 TCGA-AB-3002 TCGA-AB-3008 
        1.02        47.05        27.02 

$subtype4
TCGA-AB-2806 TCGA-AB-2810 TCGA-AB-2812 TCGA-AB-2814 TCGA-AB-2820 TCGA-AB-2822 
       31.07         1.02        12.03        26.04         0.00        31.99 
TCGA-AB-2839 TCGA-AB-2844 TCGA-AB-2849 TCGA-AB-2853 TCGA-AB-2858 TCGA-AB-2863 
       15.98         4.01        72.99         2.93        18.97         1.02 
TCGA-AB-2874 TCGA-AB-2875 TCGA-AB-2876 TCGA-AB-2879 TCGA-AB-2886 TCGA-AB-2889 
       13.02         6.97        40.08         8.05         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-2934 TCGA-AB-2937 TCGA-AB-2942 TCGA-AB-2955 
       12.03        15.02         0.92         7.07        21.07        16.08 
TCGA-AB-2957 TCGA-AB-2964 TCGA-AB-2966 TCGA-AB-2977 TCGA-AB-2979 TCGA-AB-2984 
       20.02        41.98        28.08         1.02        22.06        38.04 
TCGA-AB-2986 TCGA-AB-2993 TCGA-AB-3000 TCGA-AB-3009 TCGA-AB-3011 
        6.97        25.02        41.06        18.97        61.97 

subtype1 subtype2 subtype3 subtype4 
       0        0        0        0 
subtype1 subtype2 subtype3 subtype4 
   69.04    62.04    94.06    72.99 
subtype1 subtype2 subtype3 subtype4 
    8.05    13.48    11.01    15.98 
[1] "0.0 - 69.0 (8.1)"  "0.0 - 62.0 (13.5)" "0.0 - 94.1 (11.0)"
[4] "0.0 - 73.0 (16.0)"
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 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"
