[1] "ofn"          "-oTGBMLGG-TP"
[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/GBMLGG-TP/22506567/GBMLGG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBMLGG-TP/22573865/GBMLGG-TP.mergedcluster.txt"

nPatients in clinical file=1110, in cluster file=1114, common to both=1109
[1]   14 1109
[1] "MRNA_CNMF"
[1] 3
  1   2   3   4 
167  97 139 122 
  1   2   3   4 
167  97 139 122 
[1] "MRNA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
153 107 103 162 
  1   2   3   4 
153 107 103 162 
[1] "MIR_CNMF"
[1] 3
  1   2   3   4 
151 189  93 130 
  1   2   3   4 
151 189  93 130 
[1] "MIR_CHIERARCHICAL"
[1] 3
  1   2   3 
303 129 131 
  1   2   3 
303 129 131 
[1] "CN_CNMF"
[1] 3
  1   2   3 
528 468  89 
  1   2   3 
528 468  89 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
179 225  88 161 
  1   2   3   4 
179 225  88 161 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
219 171 161 109 
  1   2   3   4 
219 171 161 109 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
241 256 163 
  1   2   3 
241 256 163 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
250 190 227 
  1   2   3 
250 190 227 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
208 190 269 
  1   2   3 
208 190 269 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
140 106  83 182 
  1   2   3   4 
140 106  83 182 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
222 186 103 
  1   2   3 
222 186 103 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4 
126 119 106 156 
  1   2   3   4 
126 119 106 156 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 98  77 120  57  63  92 
  1   2   3   4   5   6 
 98  77 120  57  63  92 
[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] "RADIATION_THERAPY"                   
[10] "KARNOFSKY_PERFORMANCE_SCORE"         
[11] "HISTOLOGICAL_TYPE"                   
[12] "RACE"                                
[13] "ETHNICITY"                           

Input Data has 13 rows and 1109 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=74,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=482,	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=414,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=25,	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:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'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 1109 columns, 1 survival variables, and 8 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "TUMOR_TISSUE_SITE"          
[3] "GENDER"                      "RADIATION_THERAPY"          
[5] "KARNOFSKY_PERFORMANCE_SCORE" "HISTOLOGICAL_TYPE"          
[7] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=74, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  18 149
  subtype2  14  83
  subtype3  24 114
  subtype4  19 102
subtype1 subtype2 subtype3 subtype4 
     167       97      138      121 
subtype1 subtype2 subtype3 subtype4 
     149       83      114      102 
$subtype1
TCGA-06-5410 TCGA-06-5412 TCGA-06-5418 TCGA-12-1092 TCGA-12-5295 TCGA-14-0736 
        3.55         4.54         2.73        21.73        14.93        15.12 
TCGA-14-0781 TCGA-14-0783 TCGA-14-1034 TCGA-14-1396 TCGA-14-1452 TCGA-14-1823 
        0.95         6.21        15.95         1.12         7.10        17.85 
TCGA-14-1829 TCGA-14-2554 TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-19-1787 
        7.17        17.49        29.03        10.29         9.14        12.66 
TCGA-19-1790 TCGA-19-2623 TCGA-19-5947 TCGA-19-5955 TCGA-26-1438 TCGA-27-1830 
        5.06         7.53         6.64         1.78        10.03         5.06 
TCGA-27-1831 TCGA-27-1832 TCGA-27-1838 TCGA-27-2524 TCGA-27-2527 TCGA-28-1745 
       16.60         9.86        11.51         7.59        14.40        11.34 
TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1760 TCGA-28-2502 TCGA-28-2509 
        8.35         7.63         8.48         4.70         0.66         4.77 
TCGA-32-1977 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 
        0.10        19.50         4.67        12.69        14.86        12.23 
TCGA-32-2494 TCGA-32-2615 TCGA-32-2632 TCGA-32-4208 TCGA-32-4209 TCGA-32-4213 
       20.78        15.95         8.84        21.14        20.32        19.86 
TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-76-4926 TCGA-76-4927 TCGA-76-6193 
        4.44        11.84         0.20         4.54        17.59         2.70 
TCGA-76-6282 TCGA-02-0001 TCGA-02-0003 TCGA-02-0004 TCGA-02-0009 TCGA-02-0025 
       17.06        11.77         4.73        11.34        10.59        42.74 
TCGA-02-0027 TCGA-02-0028 TCGA-02-0033 TCGA-02-0034 TCGA-02-0039 TCGA-02-0043 
       12.16        90.58         2.83        14.14        10.52        18.31 
TCGA-02-0046 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
        6.87        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 
        9.57         6.02        19.73        20.84        27.25         8.81 
TCGA-02-0089 TCGA-02-0099 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0337 
       16.96         3.48        11.67        17.65        23.18        25.12 
TCGA-02-0456 TCGA-02-2470 TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0130 
        3.35        12.92        20.32         6.15        20.38        12.95 
TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 TCGA-06-0147 TCGA-06-0149 
       11.90         0.20        10.29        11.74        17.79         8.61 
TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 TCGA-06-0164 TCGA-06-0168 
       12.33        13.94        10.45         5.85        56.91        19.66 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0184 TCGA-06-0189 TCGA-06-0190 
        3.29         4.04        91.00        69.90        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 TCGA-06-0210 
       38.96         4.67         5.56         0.39         7.66         7.40 
TCGA-06-0213 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 
        0.53         9.01        72.36         9.57        12.62         5.75 
TCGA-06-0646 TCGA-06-0649 TCGA-06-0650 TCGA-06-0750 TCGA-06-0878 TCGA-06-0881 
        5.75         2.10        23.57         0.92         7.17        16.57 
TCGA-06-0939 TCGA-06-1084 TCGA-06-1800 TCGA-06-1802 TCGA-08-0346 TCGA-08-0352 
       26.76        23.93        26.79        15.32         8.42         1.28 
TCGA-08-0360 TCGA-08-0373 TCGA-08-0390 TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 
       15.39         4.41        13.97         0.72        12.56         4.27 
TCGA-08-0512 TCGA-08-0522 TCGA-08-0525 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 
       42.15        20.88        15.98        34.92        10.45         7.59 
TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 TCGA-12-0778 TCGA-12-0822 
       53.85        43.23         7.63         9.73        14.93        23.51 
TCGA-12-0829 TCGA-12-1088 TCGA-12-1093 TCGA-12-1095 TCGA-12-1096 TCGA-14-0789 
       20.58       127.59        15.98        15.85         9.11        11.24 
TCGA-14-0817 TCGA-14-1037 TCGA-19-1385 TCGA-19-1389 TCGA-26-5139 TCGA-28-2513 
        5.39        19.30        10.75         4.64         1.58         7.30 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5214 TCGA-28-5215 
       11.28        17.88        14.53        23.44        11.01 

$subtype2
TCGA-06-5413 TCGA-06-5416 TCGA-06-5856 TCGA-06-5858 TCGA-12-1598 TCGA-12-3644 
        8.81         6.71         3.75         6.15        15.65        59.77 
TCGA-12-3646 TCGA-12-3650 TCGA-12-5301 TCGA-14-0865 TCGA-14-1453 TCGA-14-1454 
       44.02        10.95         2.04        16.50         1.15        30.18 
TCGA-14-1455 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 TCGA-14-3477 
        0.92         0.99         1.97        17.79         7.63         3.78 
TCGA-14-4157 TCGA-19-1390 TCGA-19-1392 TCGA-19-2624 TCGA-19-5956 TCGA-26-1799 
        3.42        25.38         3.65         0.16        22.49         9.37 
TCGA-26-5135 TCGA-26-5136 TCGA-27-2521 TCGA-27-2523 TCGA-28-1753 TCGA-28-1755 
        8.88        18.97        16.77        16.08         1.22         1.55 
TCGA-32-1973 TCGA-32-5222 TCGA-41-5651 TCGA-76-4929 TCGA-76-4932 TCGA-76-4934 
       21.07        19.23        15.12         3.65        47.93         2.53 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6285 TCGA-02-0007 TCGA-02-0010 TCGA-02-0011 
       36.85        16.70         8.35        23.18        35.41        20.71 
TCGA-02-0014 TCGA-02-0015 TCGA-02-0021 TCGA-02-0024 TCGA-02-0026 TCGA-02-0038 
       82.59        20.61        77.65        53.10        24.59        10.72 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0069 TCGA-02-0074 TCGA-02-0083 TCGA-02-0104 
       14.73         3.22        28.70        10.19        22.72        65.00 
TCGA-02-0114 TCGA-02-0116 TCGA-02-0266 TCGA-02-0271 TCGA-02-0281 TCGA-02-0321 
       99.98        48.95        17.72        14.47         3.98         9.90 
TCGA-02-0338 TCGA-02-0339 TCGA-02-2466 TCGA-02-2483 TCGA-06-0173 TCGA-06-0174 
       10.59        12.39        16.80        15.32         4.47         3.22 
TCGA-06-0177 TCGA-06-0182 TCGA-06-0241 TCGA-06-0410 TCGA-06-0413 TCGA-06-0414 
        4.18         3.65        48.69         4.70         3.16        35.11 
TCGA-06-0686 TCGA-06-0745 TCGA-06-0875 TCGA-06-1086 TCGA-06-1087 TCGA-06-2559 
       14.20         7.86        43.46         6.84         4.04         4.93 
TCGA-06-2569 TCGA-08-0245 TCGA-08-0344 TCGA-08-0353 TCGA-08-0517 TCGA-08-0524 
        0.43        37.84       115.86         8.42        58.68         7.27 
TCGA-12-0616 TCGA-12-0692 TCGA-12-0820 TCGA-12-0821 TCGA-14-0867 TCGA-14-0871 
       14.73         3.65        18.48        10.62         2.04        28.93 
TCGA-16-0850 TCGA-26-5133 TCGA-26-5134 TCGA-28-5213 TCGA-28-5216 TCGA-28-5218 
       16.37        14.86         5.49        31.27        13.64         5.16 
TCGA-32-2616 
        7.36 

$subtype3
TCGA-06-5408 TCGA-06-5414 TCGA-06-5415 TCGA-12-1599 TCGA-12-1600 TCGA-12-3648 
       11.74         8.98         8.55        25.68        14.73        26.93 
TCGA-12-3649 TCGA-12-3652 TCGA-12-3653 TCGA-12-5299 TCGA-14-0786 TCGA-14-0790 
       15.22        34.92        14.53         3.22        23.05        13.78 
TCGA-14-0866 TCGA-14-1402 TCGA-14-1459 TCGA-14-2555 TCGA-16-1047 TCGA-16-1056 
       26.33        32.05        12.43         7.96         4.57        14.01 
TCGA-16-1062 TCGA-16-1063 TCGA-19-0964 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 
       21.24        13.97         3.39         7.17         3.25         0.13 
TCGA-19-2619 TCGA-19-2620 TCGA-19-2621 TCGA-19-2625 TCGA-19-2631 TCGA-19-4068 
        9.67         4.87         1.08         4.08         7.00         4.50 
TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5954 TCGA-19-5958 TCGA-19-5959 
       17.19         8.02        18.90        12.10        14.07        16.80 
TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-5132 TCGA-27-1833 TCGA-27-1835 
       13.87         9.73         7.13         9.40        24.23        21.30 
TCGA-27-1837 TCGA-27-2526 TCGA-27-2528 TCGA-28-1749 TCGA-28-1757 TCGA-32-1970 
       14.04         2.86        15.78         9.21         0.13        15.39 
TCGA-32-1978 TCGA-32-1991 TCGA-32-2495 TCGA-32-2638 TCGA-32-4719 TCGA-41-2572 
       15.85        16.93        15.02        25.18        10.85        13.35 
TCGA-41-3392 TCGA-76-4928 TCGA-76-4931 TCGA-02-0016 TCGA-02-0023 TCGA-02-0068 
        0.99         3.09         9.17        87.06        20.12        26.43 
TCGA-02-0070 TCGA-02-0071 TCGA-02-0102 TCGA-02-0113 TCGA-02-0260 TCGA-02-0269 
       25.05         5.49        27.02        92.65        16.93        10.75 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0333 TCGA-02-0422 
       13.87        14.20        15.95        12.23         4.37        14.50 
TCGA-02-0430 TCGA-02-2485 TCGA-06-0125 TCGA-06-0126 TCGA-06-0137 TCGA-06-0145 
       10.55        15.45        47.61         6.94        26.70         2.33 
TCGA-06-0148 TCGA-06-0157 TCGA-06-0158 TCGA-06-0185 TCGA-06-0187 TCGA-06-0208 
       10.09         3.19        10.82        73.84        27.22         8.42 
TCGA-06-0211 TCGA-06-0216 TCGA-06-0394 TCGA-06-0402 TCGA-06-0743 TCGA-06-0744 
       11.84        24.16        10.82         0.26        26.40        46.88 
TCGA-06-0747 TCGA-06-0876 TCGA-06-0879 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
        2.70        46.19        40.41        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2566 TCGA-06-6390 TCGA-08-0244 TCGA-08-0246 TCGA-08-0354 
       16.64         5.98         5.39        22.68         4.18        17.95 
TCGA-08-0355 TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0386 
       24.56        31.10        37.58        22.29        12.23        18.02 
TCGA-08-0511 TCGA-08-0514 TCGA-08-0516 TCGA-08-0518 TCGA-08-0521 TCGA-08-0529 
        7.73        11.08        19.59        19.33         4.80        18.41 
TCGA-08-0531 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0703 TCGA-12-0707 
        7.56        94.78         0.10        26.66        20.38        28.41 
TCGA-12-0780 TCGA-12-0826 TCGA-12-0828 TCGA-12-1090 TCGA-12-1091 TCGA-12-1094 
       14.86        27.78         8.94         7.59        33.21        12.23 
TCGA-12-1098 TCGA-14-0787 TCGA-15-0742 TCGA-15-1446 TCGA-19-0955 TCGA-19-0962 
        3.98         2.24        13.78        19.10        11.77         0.66 
TCGA-19-1386 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-81-5910 TCGA-87-5896 
        9.07        22.68        12.76         5.42         1.61        26.30 

$subtype4
TCGA-06-6391 TCGA-06-5411 TCGA-06-5417 TCGA-06-5859 TCGA-12-1597 TCGA-12-1602 
        1.48         8.35         5.10         4.57        22.19         6.77 
TCGA-12-3651 TCGA-14-0812 TCGA-14-1401 TCGA-14-1451 TCGA-14-1456 TCGA-14-1458 
       12.69         3.25         3.75        23.11        40.96         6.67 
TCGA-14-1827 TCGA-14-3476 TCGA-16-0848 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
        5.88         0.39        17.59         6.41         8.61        14.27 
TCGA-19-1788 TCGA-19-2629 TCGA-19-5960 TCGA-27-1834 TCGA-27-1836 TCGA-27-2518 
        3.68        24.23        14.96        40.54        30.05        24.76 
TCGA-27-2519 TCGA-28-1746 TCGA-28-1747 TCGA-28-1756 TCGA-28-2506 TCGA-32-1976 
       18.08         0.20         2.53         2.83         6.74         0.49 
TCGA-32-1980 TCGA-32-2634 TCGA-32-4210 TCGA-32-4211 TCGA-41-2571 TCGA-41-2573 
        1.18        22.78         3.72        12.59         0.85         8.94 
TCGA-41-2575 TCGA-76-4925 TCGA-76-6192 TCGA-02-0080 TCGA-02-0084 TCGA-02-0085 
        9.53         4.80         3.29        89.72        12.62        51.32 
TCGA-02-0087 TCGA-02-0115 TCGA-02-0258 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 
       57.76        15.65        16.54         7.73        10.62         7.33 
TCGA-02-0330 TCGA-02-0332 TCGA-02-0432 TCGA-02-0439 TCGA-02-0440 TCGA-02-0446 
       15.91        25.71        47.11         0.66        11.34         9.27 
TCGA-02-0451 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 TCGA-06-0132 TCGA-06-0133 
       16.21         3.98        22.72        33.67        25.35        14.30 
TCGA-06-0138 TCGA-06-0142 TCGA-06-0146 TCGA-06-0160 TCGA-06-0162 TCGA-06-0166 
       24.23         2.20        20.09        11.80         3.42         5.85 
TCGA-06-0167 TCGA-06-0171 TCGA-06-0178 TCGA-06-0179 TCGA-06-0188 TCGA-06-0195 
       11.41        13.12        88.14        20.25        44.58         7.40 
TCGA-06-0214 TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 
       15.02         0.72        19.82        13.64        13.32        20.42 
TCGA-06-0648 TCGA-06-0749 TCGA-06-0882 TCGA-06-1801 TCGA-06-1804 TCGA-06-1805 
        9.80         2.70        20.78        11.84        13.61        33.90 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2561 TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 
        1.08        12.49        17.65         4.37        31.50         7.79 
TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 TCGA-08-0351 
        1.74        25.71        12.16         9.80        29.23        65.33 
TCGA-08-0359 TCGA-08-0380 TCGA-08-0385 TCGA-08-0389 TCGA-08-0520 TCGA-12-0618 
        3.39        14.93         2.70        15.35        10.75        12.99 
TCGA-12-0670 TCGA-12-0818 TCGA-12-0819 TCGA-12-0827 TCGA-12-1089 TCGA-12-1097 
       25.97        91.76        24.79        38.76         5.82        14.53 
TCGA-12-1099 TCGA-14-0813 TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 
        4.14         1.35        50.53        53.19        13.28         3.91 
TCGA-16-0849 TCGA-19-0957 TCGA-19-1387 TCGA-19-1388 TCGA-26-1442 TCGA-28-2514 
       26.07        21.90         5.95        12.95        31.33         5.26 
TCGA-28-5204 
       14.93 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.16     0.10     0.20 
subtype1 subtype2 subtype3 subtype4 
  127.59   115.86    94.78    91.76 
subtype1 subtype2 subtype3 subtype4 
  11.340   13.640   13.825   12.690 
[1] "0.1 - 127.6 (11.3)" "0.2 - 115.9 (13.6)" "0.1 - 94.8 (13.8)" 
[4] "0.2 - 91.8 (12.7)" 
D1V2, continuous
D1V3, binary
          cls
clus         0
  subtype1 167
  subtype2  97
  subtype3 139
  subtype4 122
[1] "NOT AVAILABLE: table only has an event [0]"
D1V4, binary
          cls
clus         0   1
  subtype1  63 104
  subtype2  44  53
  subtype3  60  79
  subtype4  38  84
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  104
  subtype2   44   53
  subtype3   60   79
  subtype4   38   84
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       63       44       60       38
  MALE        104       53       79       84
[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"
D1V5, binary
          cls
clus         0   1
  subtype1  21 138
  subtype2  16  77
  subtype3  14 121
  subtype4  19  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21  138
  subtype2   16   77
  subtype3   14  121
  subtype4   19   99
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       16       14       19
  YES      138       77      121       99
[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"
D1V6, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             1                   8
  subtype2                             0                   8
  subtype3                             0                   3
  subtype4                             5                   1
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             158
  subtype2                              89
  subtype3                             136
  subtype4                             116
D1V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0        5
  TREATED PRIMARY GBM                    8        8        3        1
  UNTREATED PRIMARY (DE NOVO) GBM      158       89      136      116
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        12   146
  subtype2     2                         7    84
  subtype3     4                         7   125
  subtype4     3                         5   107
D1V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        4        3
  BLACK OR AFRICAN AMERICAN       12        7        7        5
  WHITE                          146       84      125      107
[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"
D1V9, binary
          cls
clus         0   1
  subtype1   3 139
  subtype2   5  72
  subtype3   3 121
  subtype4   1 106
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  139
  subtype2    5   72
  subtype3    3  121
  subtype4    1  106
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        5        3        1
  NOT HISPANIC OR LATINO      139       72      121      106
[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 = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2        0   1
  subtype1  15 138
  subtype2  26  81
  subtype3  16  86
  subtype4  18 143
subtype1 subtype2 subtype3 subtype4 
     153      107      102      161 
subtype1 subtype2 subtype3 subtype4 
     138       81       86      143 
$subtype1
TCGA-06-5410 TCGA-06-5412 TCGA-06-5418 TCGA-14-0736 TCGA-14-0781 TCGA-14-0783 
        3.55         4.54         2.73        15.12         0.95         6.21 
TCGA-14-1034 TCGA-14-1396 TCGA-14-1452 TCGA-16-1045 TCGA-16-1060 TCGA-19-1790 
       15.95         1.12         7.10        29.03         9.14         5.06 
TCGA-19-5947 TCGA-19-5952 TCGA-19-5955 TCGA-26-1438 TCGA-26-1439 TCGA-26-5136 
        6.64        18.90         1.78        10.03        13.87        18.97 
TCGA-27-1832 TCGA-27-2524 TCGA-27-2527 TCGA-28-1751 TCGA-28-1760 TCGA-28-2502 
        9.86         7.59        14.40         7.63         4.70         0.66 
TCGA-28-2509 TCGA-32-1977 TCGA-32-1986 TCGA-32-1987 TCGA-32-2491 TCGA-32-2494 
        4.77         0.10        12.69        14.86        12.23        20.78 
TCGA-32-2638 TCGA-32-4209 TCGA-76-4926 TCGA-76-6193 TCGA-76-6282 TCGA-02-0001 
       25.18        20.32         4.54         2.70        17.06        11.77 
TCGA-02-0003 TCGA-02-0004 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0011 
        4.73        11.34        23.18        10.59        35.41        20.71 
TCGA-02-0015 TCGA-02-0021 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0028 
       20.61        77.65        53.10        42.74        12.16        90.58 
TCGA-02-0033 TCGA-02-0034 TCGA-02-0038 TCGA-02-0039 TCGA-02-0043 TCGA-02-0046 
        2.83        14.14        10.72        10.52        18.31         6.87 
TCGA-02-0047 TCGA-02-0051 TCGA-02-0052 TCGA-02-0054 TCGA-02-0057 TCGA-02-0058 
       14.73        15.09        12.59         6.54        19.86         8.35 
TCGA-02-0059 TCGA-02-0060 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        9.57         6.02        19.73        26.43        25.05         5.49 
TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0102 TCGA-02-0106 TCGA-02-0107 
       20.84        27.25         8.81        27.02        11.67        17.65 
TCGA-02-0111 TCGA-02-0116 TCGA-02-0266 TCGA-02-0271 TCGA-02-0337 TCGA-02-0456 
       23.18        48.95        17.72        14.47        25.12         3.35 
TCGA-02-2486 TCGA-06-0122 TCGA-06-0124 TCGA-06-0130 TCGA-06-0139 TCGA-06-0141 
       20.32         6.15        20.38        12.95        11.90        10.29 
TCGA-06-0143 TCGA-06-0147 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0164 
       11.74        17.79        12.33        13.94        10.45        56.91 
TCGA-06-0169 TCGA-06-0175 TCGA-06-0176 TCGA-06-0184 TCGA-06-0189 TCGA-06-0190 
        3.29         4.04        91.00        69.90        15.42        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0206 TCGA-06-0210 TCGA-06-0394 
       38.96         4.67         5.56         7.66         7.40        10.82 
TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 TCGA-06-0645 TCGA-06-0650 
        9.01        72.36         9.57        12.62         5.75        23.57 
TCGA-06-0750 TCGA-06-0878 TCGA-06-0881 TCGA-06-1084 TCGA-06-1086 TCGA-06-2562 
        0.92         7.17        16.57        23.93         6.84        12.56 
TCGA-06-2569 TCGA-08-0346 TCGA-08-0352 TCGA-08-0356 TCGA-08-0360 TCGA-08-0390 
        0.43         8.42         1.28        31.10        15.39        13.97 
TCGA-08-0392 TCGA-08-0509 TCGA-08-0510 TCGA-08-0512 TCGA-08-0522 TCGA-08-0525 
        0.72        12.56         4.27        42.15        20.88        15.98 
TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0772 TCGA-12-0775 TCGA-12-0776 
       34.92        10.45         7.59        53.85         7.63         9.73 
TCGA-12-0778 TCGA-12-0822 TCGA-12-0829 TCGA-12-1093 TCGA-12-1094 TCGA-12-1096 
       14.93        23.51        20.58        15.98        12.23         9.11 
TCGA-14-0789 TCGA-14-0867 TCGA-14-0871 TCGA-19-1385 TCGA-19-1389 TCGA-26-5139 
       11.24         2.04        28.93        10.75         4.64         1.58 
TCGA-28-2513 TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5214 
        7.30        11.28        17.88        14.53        31.27        23.44 
TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       11.01        13.64         5.16 

$subtype2
TCGA-06-6391 TCGA-06-5416 TCGA-06-5417 TCGA-12-1597 TCGA-12-3646 TCGA-12-3650 
        1.48         6.71         5.10        22.19        44.02        10.95 
TCGA-12-3651 TCGA-14-0865 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1458 
       12.69        16.50        30.18         0.92        40.96         6.67 
TCGA-14-1821 TCGA-14-1825 TCGA-14-3477 TCGA-14-4157 TCGA-16-1460 TCGA-19-0960 
       17.79         7.63         3.78         3.42         6.41         8.61 
TCGA-19-1390 TCGA-19-1788 TCGA-19-2624 TCGA-19-2629 TCGA-19-5956 TCGA-19-5960 
       25.38         3.68         0.16        24.23        22.49        14.96 
TCGA-26-1799 TCGA-27-1836 TCGA-27-1837 TCGA-27-2521 TCGA-28-1746 TCGA-28-1756 
        9.37        30.05        14.04        16.77         0.20         2.83 
TCGA-32-1976 TCGA-32-2634 TCGA-32-4208 TCGA-32-4210 TCGA-32-5222 TCGA-41-2571 
        0.49        22.78        21.14         3.72        19.23         0.85 
TCGA-41-2573 TCGA-41-2575 TCGA-41-5651 TCGA-76-4925 TCGA-76-4932 TCGA-76-4934 
        8.94         9.53        15.12         4.80        47.93         2.53 
TCGA-76-6191 TCGA-76-6285 TCGA-02-0014 TCGA-02-0026 TCGA-02-0048 TCGA-02-0069 
       16.70         8.35        82.59        24.59         3.22        28.70 
TCGA-02-0074 TCGA-02-0080 TCGA-02-0084 TCGA-02-0087 TCGA-02-0104 TCGA-02-0114 
       10.19        89.72        12.62        57.76        65.00        99.98 
TCGA-02-0258 TCGA-02-0281 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 TCGA-02-0440 
       16.54         3.98        10.59        12.39        47.11        11.34 
TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0128 TCGA-06-0129 TCGA-06-0146 
       16.80        15.32        15.45        22.72        33.67        20.09 
TCGA-06-0166 TCGA-06-0174 TCGA-06-0188 TCGA-06-0241 TCGA-06-0410 TCGA-06-0413 
        5.85         3.22        44.58        48.69         4.70         3.16 
TCGA-06-0414 TCGA-06-0648 TCGA-06-0686 TCGA-06-0875 TCGA-06-1087 TCGA-06-1801 
       35.11         9.80        14.20        43.46         4.04        11.84 
TCGA-06-1805 TCGA-06-2558 TCGA-06-2559 TCGA-06-2570 TCGA-06-6389 TCGA-08-0245 
       33.90        12.49         4.93        31.50         7.79        37.84 
TCGA-08-0344 TCGA-08-0348 TCGA-08-0350 TCGA-08-0351 TCGA-08-0385 TCGA-08-0517 
      115.86        12.16        29.23        65.33         2.70        58.68 
TCGA-08-0524 TCGA-12-0616 TCGA-12-0618 TCGA-12-0818 TCGA-12-0820 TCGA-12-1099 
        7.27        14.73        12.99        91.76        18.48         4.14 
TCGA-15-1444 TCGA-15-1447 TCGA-15-1449 TCGA-16-0849 TCGA-16-0850 TCGA-19-0957 
       50.53        53.19        13.28        26.07        16.37        21.90 
TCGA-26-1442 TCGA-26-5133 TCGA-26-5134 TCGA-28-2514 TCGA-28-5204 
       31.33        14.86         5.49         5.26        14.93 

$subtype3
TCGA-06-5408 TCGA-06-5414 TCGA-12-1600 TCGA-12-3648 TCGA-12-3652 TCGA-12-3653 
       11.74         8.98        14.73        26.93        34.92        14.53 
TCGA-12-5295 TCGA-12-5299 TCGA-14-0786 TCGA-14-0790 TCGA-14-1402 TCGA-14-1453 
       14.93         3.22        23.05        13.78        32.05         1.15 
TCGA-14-2555 TCGA-16-1047 TCGA-16-1056 TCGA-16-1062 TCGA-19-0964 TCGA-19-1786 
        7.96         4.57        14.01        21.24         3.39         7.17 
TCGA-19-2619 TCGA-19-2621 TCGA-19-2631 TCGA-19-4068 TCGA-19-5950 TCGA-19-5951 
        9.67         1.08         7.00         4.50        17.19         8.02 
TCGA-19-5954 TCGA-26-1440 TCGA-26-1443 TCGA-27-1831 TCGA-27-1833 TCGA-27-1835 
       12.10         9.73         7.13        16.60        24.23        21.30 
TCGA-27-2523 TCGA-27-2526 TCGA-27-2528 TCGA-28-1749 TCGA-28-1755 TCGA-28-1757 
       16.08         2.86        15.78         9.21         1.55         0.13 
TCGA-32-1978 TCGA-32-1991 TCGA-32-2495 TCGA-32-4719 TCGA-41-2572 TCGA-76-4927 
       15.85        16.93        15.02        10.85        13.35        17.59 
TCGA-76-4928 TCGA-02-0016 TCGA-02-0083 TCGA-02-0113 TCGA-02-0260 TCGA-02-0269 
        3.09        87.06        22.72        92.65        16.93        10.75 
TCGA-02-0285 TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0333 TCGA-02-0422 
       13.87        14.20        15.95        12.23         4.37        14.50 
TCGA-02-0430 TCGA-06-0125 TCGA-06-0126 TCGA-06-0137 TCGA-06-0145 TCGA-06-0148 
       10.55        47.61         6.94        26.70         2.33        10.09 
TCGA-06-0157 TCGA-06-0182 TCGA-06-0187 TCGA-06-0211 TCGA-06-0402 TCGA-06-0743 
        3.19         3.65        27.22        11.84         0.26        26.40 
TCGA-06-0744 TCGA-06-0747 TCGA-06-0876 TCGA-06-0879 TCGA-06-2563 TCGA-06-2564 
       46.88         2.70        46.19        40.41        30.64         5.95 
TCGA-06-2565 TCGA-08-0244 TCGA-08-0246 TCGA-08-0354 TCGA-08-0355 TCGA-08-0357 
       16.64        22.68         4.18        17.95        24.56        37.58 
TCGA-08-0358 TCGA-08-0375 TCGA-08-0511 TCGA-08-0514 TCGA-08-0518 TCGA-08-0529 
       22.29        12.23         7.73        11.08        19.33        18.41 
TCGA-08-0531 TCGA-12-0656 TCGA-12-0657 TCGA-12-0688 TCGA-12-0692 TCGA-12-0703 
        7.56        94.78         0.10        26.66         3.65        20.38 
TCGA-12-0780 TCGA-12-0821 TCGA-12-0828 TCGA-12-1091 TCGA-12-1098 TCGA-14-0787 
       14.86        10.62         8.94        33.21         3.98         2.24 
TCGA-15-0742 TCGA-19-1386 TCGA-28-5219 TCGA-28-6450 TCGA-81-5910 TCGA-87-5896 
       13.78         9.07        22.68         5.42         1.61        26.30 

$subtype4
TCGA-06-5411 TCGA-06-5413 TCGA-06-5415 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.35         8.81         8.55         3.75         6.15         4.57 
TCGA-12-1092 TCGA-12-1598 TCGA-12-1599 TCGA-12-1602 TCGA-12-3644 TCGA-12-3649 
       21.73        15.65        25.68         6.77        59.77        15.22 
TCGA-12-5301 TCGA-14-0812 TCGA-14-0866 TCGA-14-1401 TCGA-14-1451 TCGA-14-1459 
        2.04         3.25        26.33         3.75        23.11        12.43 
TCGA-14-1794 TCGA-14-1795 TCGA-14-1823 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 
        0.99         1.97        17.85         5.88         7.17        17.49 
TCGA-14-3476 TCGA-16-0848 TCGA-16-1055 TCGA-16-1063 TCGA-19-0963 TCGA-19-1392 
        0.39        17.59        10.29        13.97        14.27         3.65 
TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2620 TCGA-19-2623 TCGA-19-2625 
       12.66         3.25         0.13         4.87         7.53         4.08 
TCGA-19-5958 TCGA-19-5959 TCGA-26-5132 TCGA-26-5135 TCGA-27-1830 TCGA-27-1834 
       14.07        16.80         9.40         8.88         5.06        40.54 
TCGA-27-1838 TCGA-27-2518 TCGA-27-2519 TCGA-28-1745 TCGA-28-1747 TCGA-28-1750 
       11.51        24.76        18.08        11.34         2.53         8.35 
TCGA-28-1752 TCGA-28-1753 TCGA-28-2506 TCGA-32-1970 TCGA-32-1973 TCGA-32-1979 
        8.48         1.22         6.74        15.39        21.07        19.50 
TCGA-32-1980 TCGA-32-1982 TCGA-32-2615 TCGA-32-2632 TCGA-32-4211 TCGA-32-4213 
        1.18         4.67        15.95         8.84        12.59        19.86 
TCGA-41-3392 TCGA-41-3393 TCGA-41-3915 TCGA-41-4097 TCGA-76-4929 TCGA-76-4931 
        0.99         4.44        11.84         0.20         3.65         9.17 
TCGA-76-4935 TCGA-76-6192 TCGA-02-0023 TCGA-02-0085 TCGA-02-0089 TCGA-02-0099 
       36.85         3.29        20.12        51.32        16.96         3.48 
TCGA-02-0115 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 TCGA-02-0326 TCGA-02-0330 
       15.65         9.90         7.73        10.62         7.33        15.91 
TCGA-02-0332 TCGA-02-0439 TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-06-0127 
       25.71         0.66         9.27        16.21        12.92         3.98 
TCGA-06-0132 TCGA-06-0133 TCGA-06-0138 TCGA-06-0140 TCGA-06-0142 TCGA-06-0149 
       25.35        14.30        24.23         0.20         2.20         8.61 
TCGA-06-0156 TCGA-06-0158 TCGA-06-0160 TCGA-06-0162 TCGA-06-0167 TCGA-06-0168 
        5.85        10.82        11.80         3.42        11.41        19.66 
TCGA-06-0171 TCGA-06-0173 TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0185 
       13.12         4.47         4.18        88.14        20.25        73.84 
TCGA-06-0195 TCGA-06-0201 TCGA-06-0208 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        7.40         0.39         8.42         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0646 
        0.72        19.82        13.64        13.32        20.42         5.75 
TCGA-06-0649 TCGA-06-0745 TCGA-06-0749 TCGA-06-0882 TCGA-06-0939 TCGA-06-1800 
        2.10         7.86         2.70        20.78        26.76        26.79 
TCGA-06-1802 TCGA-06-1804 TCGA-06-2557 TCGA-06-2561 TCGA-06-2566 TCGA-06-2567 
       15.32        13.61         1.08        17.65         5.98         4.37 
TCGA-06-6390 TCGA-08-0345 TCGA-08-0347 TCGA-08-0349 TCGA-08-0353 TCGA-08-0359 
        5.39         1.74        25.71         9.80         8.42         3.39 
TCGA-08-0373 TCGA-08-0380 TCGA-08-0386 TCGA-08-0389 TCGA-08-0516 TCGA-08-0520 
        4.41        14.93        18.02        15.35        19.59        10.75 
TCGA-08-0521 TCGA-12-0670 TCGA-12-0707 TCGA-12-0773 TCGA-12-0819 TCGA-12-0826 
        4.80        25.97        28.41        43.23        24.79        27.78 
TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1095 TCGA-12-1097 
       38.76       127.59         5.82         7.59        15.85        14.53 
TCGA-14-0813 TCGA-14-0817 TCGA-14-1037 TCGA-15-1446 TCGA-16-0846 TCGA-19-0955 
        1.35         5.39        19.30        19.10         3.91        11.77 
TCGA-19-0962 TCGA-19-1387 TCGA-19-1388 TCGA-28-5220 TCGA-32-2616 
        0.66         5.95        12.95        12.76         7.36 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.16     0.10     0.13 
subtype1 subtype2 subtype3 subtype4 
   91.00   115.86    94.78   127.59 
subtype1 subtype2 subtype3 subtype4 
   12.23    14.86    13.78    10.62 
[1] "0.1 - 91.0 (12.2)"  "0.2 - 115.9 (14.9)" "0.1 - 94.8 (13.8)" 
[4] "0.1 - 127.6 (10.6)"
D2V2, continuous
D2V3, binary
          cls
clus         0
  subtype1 153
  subtype2 107
  subtype3 103
  subtype4 162
[1] "NOT AVAILABLE: table only has an event [0]"
D2V4, binary
          cls
clus         0   1
  subtype1  51 102
  subtype2  44  63
  subtype3  50  53
  subtype4  60 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51  102
  subtype2   44   63
  subtype3   50   53
  subtype4   60  102
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       51       44       50       60
  MALE        102       63       53      102
[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"
D2V5, binary
          cls
clus         0   1
  subtype1  17 131
  subtype2  13  91
  subtype3  11  88
  subtype4  29 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  131
  subtype2   13   91
  subtype3   11   88
  subtype4   29  125
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       13       11       29
  YES      131       91       88      125
[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"
D2V6, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             0                  11
  subtype2                             1                   3
  subtype3                             0                   3
  subtype4                             5                   3
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             142
  subtype2                             103
  subtype3                             100
  subtype4                             154
D2V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          0        1        0        5
  TREATED PRIMARY GBM                   11        3        3        3
  UNTREATED PRIMARY (DE NOVO) GBM      142      103      100      154
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        13   130
  subtype2     4                         6    95
  subtype3     3                         4    93
  subtype4     2                         8   144
D2V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        4        3        2
  BLACK OR AFRICAN AMERICAN       13        6        4        8
  WHITE                          130       95       93      144
[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"
D2V9, binary
          cls
clus         0   1
  subtype1   5 124
  subtype2   1  91
  subtype3   2  90
  subtype4   4 133
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  124
  subtype2    1   91
  subtype3    2   90
  subtype4    4  133
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        1        2        4
  NOT HISPANIC OR LATINO      124       91       90      133
[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 = MIR_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1  21 130
  subtype2  34 155
  subtype3  14  78
  subtype4  23 106
subtype1 subtype2 subtype3 subtype4 
     151      189       92      129 
subtype1 subtype2 subtype3 subtype4 
     130      155       78      106 
$subtype1
TCGA-06-5414 TCGA-06-5418 TCGA-06-5858 TCGA-06-6697 TCGA-06-6698 TCGA-12-1599 
        8.98         2.73         6.15        12.85         4.77        25.68 
TCGA-12-3649 TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0781 
       15.22        14.93         3.22         2.04        15.12         0.95 
TCGA-14-0862 TCGA-14-1034 TCGA-14-1450 TCGA-14-1452 TCGA-14-1459 TCGA-14-1823 
        2.89        15.95        58.78         7.10        12.43        17.85 
TCGA-14-1829 TCGA-16-1045 TCGA-16-1055 TCGA-16-1060 TCGA-19-1790 TCGA-19-2619 
        7.17        29.03        10.29         9.14         5.06         9.67 
TCGA-19-2621 TCGA-19-2623 TCGA-19-5947 TCGA-19-5952 TCGA-19-5954 TCGA-19-5955 
        1.08         7.53         6.64        18.90        12.10         1.78 
TCGA-19-5958 TCGA-26-1438 TCGA-26-1439 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 
       14.07        10.03        13.87        16.60         9.86        40.54 
TCGA-27-2526 TCGA-27-2527 TCGA-27-2528 TCGA-28-1745 TCGA-28-1751 TCGA-28-2502 
        2.86        14.40        15.78        11.34         7.63         0.66 
TCGA-28-2509 TCGA-32-1979 TCGA-32-1987 TCGA-32-1991 TCGA-32-2632 TCGA-32-2638 
        4.77        19.50        14.86        16.93         8.84        25.18 
TCGA-32-4213 TCGA-41-3915 TCGA-74-6575 TCGA-74-6578 TCGA-76-4927 TCGA-76-4932 
       19.86        11.84        20.91        14.33        17.59        47.93 
TCGA-76-6193 TCGA-76-6282 TCGA-76-6657 TCGA-76-6662 TCGA-02-0001 TCGA-02-0004 
        2.70        17.06         5.03        34.45        11.77        11.34 
TCGA-02-0006 TCGA-02-0009 TCGA-02-0015 TCGA-02-0027 TCGA-02-0033 TCGA-02-0037 
       18.35        10.59        20.61        12.16         2.83         3.62 
TCGA-02-0038 TCGA-02-0039 TCGA-02-0051 TCGA-02-0054 TCGA-02-0055 TCGA-02-0057 
       10.72        10.52        15.09         6.54         2.50        19.86 
TCGA-02-0059 TCGA-02-0075 TCGA-02-0079 TCGA-02-0086 TCGA-02-0115 TCGA-02-0289 
        9.57        20.84        27.25         8.81        15.65        14.20 
TCGA-02-0290 TCGA-02-0326 TCGA-02-0422 TCGA-02-2486 TCGA-06-0122 TCGA-06-0147 
       15.95         7.33        14.50        20.32         6.15        17.79 
TCGA-06-0151 TCGA-06-0159 TCGA-06-0176 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 
       46.59         9.44        91.00        69.90        27.22        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0197 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 
       38.96         4.67         5.56        11.84         0.53        15.02 
TCGA-06-0394 TCGA-06-0397 TCGA-06-0412 TCGA-06-0644 TCGA-06-0649 TCGA-06-0745 
       10.82         9.01         9.57        12.62         2.10         7.86 
TCGA-06-0749 TCGA-06-1800 TCGA-06-2561 TCGA-06-2562 TCGA-06-6390 TCGA-08-0244 
        2.70        26.79        17.65        12.56         5.39        22.68 
TCGA-08-0246 TCGA-08-0346 TCGA-08-0352 TCGA-08-0354 TCGA-08-0360 TCGA-08-0380 
        4.18         8.42         1.28        17.95        15.39        14.93 
TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0511 TCGA-08-0512 TCGA-08-0514 
       13.97        12.56         4.27         7.73        42.15        11.08 
TCGA-08-0518 TCGA-08-0521 TCGA-08-0522 TCGA-08-0525 TCGA-08-0529 TCGA-12-0657 
       19.33         4.80        20.88        15.98        18.41         0.10 
TCGA-12-0662 TCGA-12-0776 TCGA-12-0822 TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 
       38.17         9.73        23.51        27.78         8.94        20.58 
TCGA-12-1094 TCGA-12-1095 TCGA-12-1097 TCGA-14-0789 TCGA-14-1037 TCGA-14-1043 
       12.23        15.85        14.53        11.24        19.30         0.79 
TCGA-15-0742 TCGA-19-0955 TCGA-19-0962 TCGA-19-1385 TCGA-19-1386 TCGA-19-1388 
       13.78        11.77         0.66        10.75         9.07        12.95 
TCGA-19-1389 TCGA-26-5139 TCGA-28-2513 TCGA-28-5204 TCGA-28-5208 TCGA-32-2616 
        4.64         1.58         7.30        14.93        17.88         7.36 
TCGA-81-5911 
       17.72 

$subtype2
TCGA-06-5408 TCGA-06-5413 TCGA-06-5416 TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 
       11.74         8.81         6.71         5.10         3.75         4.57 
TCGA-06-6695 TCGA-06-6699 TCGA-06-6701 TCGA-12-1598 TCGA-12-1600 TCGA-12-3646 
        8.32         1.55         4.96        15.65        14.73        44.02 
TCGA-12-3648 TCGA-12-3650 TCGA-12-3653 TCGA-14-0786 TCGA-14-0790 TCGA-14-0865 
       26.93        10.95        14.53        23.05        13.78        16.50 
TCGA-14-1395 TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 TCGA-14-1821 
        1.38         1.15        30.18         0.92        40.96        17.79 
TCGA-14-1825 TCGA-14-2554 TCGA-14-3477 TCGA-14-4157 TCGA-16-0848 TCGA-16-1047 
        7.63        17.49         3.78         3.42        17.59         4.57 
TCGA-16-1056 TCGA-16-1062 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0964 
       14.01        21.24        13.97         6.41         8.61         3.39 
TCGA-19-1390 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2624 
       25.38         7.17        12.66         3.25         0.13         0.16 
TCGA-19-2629 TCGA-19-2631 TCGA-19-5950 TCGA-19-5951 TCGA-19-5953 TCGA-19-5956 
       24.23         7.00        17.19         8.02         4.73        22.49 
TCGA-19-5959 TCGA-19-5960 TCGA-26-1440 TCGA-26-5135 TCGA-26-5136 TCGA-27-1833 
       16.80        14.96         9.73         8.88        18.97        24.23 
TCGA-27-1835 TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-28-1746 TCGA-28-1747 
       21.30        18.08        16.77        16.08         0.20         2.53 
TCGA-28-1749 TCGA-32-1970 TCGA-32-1976 TCGA-32-2634 TCGA-32-4208 TCGA-32-4209 
        9.21        15.39         0.49        22.78        21.14        20.32 
TCGA-32-4210 TCGA-32-4211 TCGA-32-5222 TCGA-41-2575 TCGA-41-3393 TCGA-41-4097 
        3.72        12.59        19.23         9.53         4.44         0.20 
TCGA-41-5651 TCGA-74-6573 TCGA-74-6577 TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 
       15.12         3.45         4.34         4.80         3.65         9.17 
TCGA-76-6191 TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-02-0003 TCGA-02-0007 
       16.70         8.35        20.98         4.83         4.73        23.18 
TCGA-02-0010 TCGA-02-0014 TCGA-02-0016 TCGA-02-0026 TCGA-02-0043 TCGA-02-0048 
       35.41        82.59        87.06        24.59        18.31         3.22 
TCGA-02-0069 TCGA-02-0074 TCGA-02-0080 TCGA-02-0083 TCGA-02-0084 TCGA-02-0087 
       28.70        10.19        89.72        22.72        12.62        57.76 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0104 TCGA-02-0114 TCGA-02-0116 TCGA-02-0258 
        3.48        27.02        65.00        99.98        48.95        16.54 
TCGA-02-0260 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0324 TCGA-02-0430 
       16.93        10.75        14.47         3.98         7.73        10.55 
TCGA-02-0440 TCGA-02-2466 TCGA-02-2483 TCGA-02-2485 TCGA-06-0125 TCGA-06-0128 
       11.34        16.80        15.32        15.45        47.61        22.72 
TCGA-06-0129 TCGA-06-0137 TCGA-06-0138 TCGA-06-0145 TCGA-06-0157 TCGA-06-0158 
       33.67        26.70        24.23         2.33         3.19        10.82 
TCGA-06-0173 TCGA-06-0174 TCGA-06-0178 TCGA-06-0182 TCGA-06-0185 TCGA-06-0208 
        4.47         3.22        88.14         3.65        73.84         8.42 
TCGA-06-0216 TCGA-06-0237 TCGA-06-0402 TCGA-06-0410 TCGA-06-0646 TCGA-06-0648 
       24.16        13.64         0.26         4.70         5.75         9.80 
TCGA-06-0875 TCGA-06-0879 TCGA-06-1087 TCGA-06-2557 TCGA-06-2559 TCGA-06-2565 
       43.46        40.41         4.04         1.08         4.93        16.64 
TCGA-06-2567 TCGA-06-2570 TCGA-06-6389 TCGA-08-0245 TCGA-08-0344 TCGA-08-0345 
        4.37        31.50         7.79        37.84       115.86         1.74 
TCGA-08-0349 TCGA-08-0350 TCGA-08-0355 TCGA-08-0357 TCGA-08-0375 TCGA-08-0385 
        9.80        29.23        24.56        37.58        12.23         2.70 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0516 TCGA-08-0517 TCGA-08-0520 TCGA-08-0531 
       18.02        15.35        19.59        58.68        10.75         7.56 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0707 
       12.99        34.92        25.97        12.13         3.65        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0820 TCGA-12-0821 
       15.06        53.85        43.23         7.63        18.48        10.62 
TCGA-12-0827 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 TCGA-12-1091 TCGA-12-1098 
       38.76       127.59         5.82         7.59        33.21         3.98 
TCGA-14-0787 TCGA-14-0817 TCGA-15-1444 TCGA-16-0849 TCGA-16-0850 TCGA-26-5133 
        2.24         5.39        50.53        26.07        16.37        14.86 
TCGA-28-2514 TCGA-28-5207 TCGA-28-5209 TCGA-28-5215 TCGA-28-5220 TCGA-28-6450 
        5.26        11.28        14.53        11.01        12.76         5.42 
TCGA-76-6283 TCGA-76-6660 TCGA-87-5896 
        5.42         3.75        26.30 

$subtype3
TCGA-06-6391 TCGA-06-5411 TCGA-06-5415 TCGA-06-6388 TCGA-06-6700 TCGA-12-1597 
        1.48         8.35         8.55         5.23         4.77        22.19 
TCGA-14-0812 TCGA-14-0866 TCGA-14-1451 TCGA-14-1458 TCGA-14-1827 TCGA-14-3476 
        3.25        26.33        23.11         6.67         5.88         0.39 
TCGA-19-0963 TCGA-19-1392 TCGA-19-1788 TCGA-19-2620 TCGA-26-1799 TCGA-27-1836 
       14.27         3.65         3.68         4.87         9.37        30.05 
TCGA-27-1837 TCGA-27-2518 TCGA-28-1752 TCGA-28-1756 TCGA-28-2506 TCGA-32-1973 
       14.04        24.76         8.48         2.83         6.74        21.07 
TCGA-32-1980 TCGA-32-2495 TCGA-41-2573 TCGA-41-3392 TCGA-74-6584 TCGA-76-4926 
        1.18        15.02         8.94         0.99         7.50         4.54 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6192 TCGA-76-6663 TCGA-02-0011 TCGA-02-0023 
        2.53        36.85         3.29        18.64        20.71        20.12 
TCGA-02-0024 TCGA-02-0052 TCGA-02-0058 TCGA-02-0060 TCGA-02-0085 TCGA-02-0089 
       53.10        12.59         8.35         6.02        51.32        16.96 
TCGA-02-0321 TCGA-02-0325 TCGA-02-0330 TCGA-02-0338 TCGA-02-0339 TCGA-02-0439 
        9.90        10.62        15.91        10.59        12.39         0.66 
TCGA-02-0446 TCGA-02-0451 TCGA-02-2470 TCGA-06-0126 TCGA-06-0142 TCGA-06-0146 
        9.27        16.21        12.92         6.94         2.20        20.09 
TCGA-06-0160 TCGA-06-0162 TCGA-06-0171 TCGA-06-0177 TCGA-06-0179 TCGA-06-0195 
       11.80         3.42        13.12         4.18        20.25         7.40 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0240 TCGA-06-0241 TCGA-06-0413 TCGA-06-0414 
        0.72        19.82        20.42        48.69         3.16        35.11 
TCGA-06-0686 TCGA-06-0747 TCGA-06-0750 TCGA-06-0882 TCGA-06-0939 TCGA-06-1801 
       14.20         2.70         0.92        20.78        26.76        11.84 
TCGA-06-1804 TCGA-06-2558 TCGA-06-2564 TCGA-06-2566 TCGA-06-6694 TCGA-08-0347 
       13.61        12.49         5.95         5.98         7.36        25.71 
TCGA-08-0348 TCGA-08-0351 TCGA-08-0359 TCGA-12-0780 TCGA-12-1099 TCGA-14-0867 
       12.16        65.33         3.39        14.86         4.14         2.04 
TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 TCGA-19-1387 TCGA-26-1442 TCGA-26-5134 
       19.10        13.28         3.91         5.95        31.33         5.49 
TCGA-26-6174 TCGA-28-5219 
        2.33        22.68 

$subtype4
TCGA-06-1806 TCGA-06-5410 TCGA-06-5412 TCGA-12-1092 TCGA-12-1602 TCGA-12-3644 
       15.32         3.55         4.54        21.73         6.77        59.77 
TCGA-12-3651 TCGA-12-3652 TCGA-14-0740 TCGA-14-0783 TCGA-14-1396 TCGA-14-1401 
       12.69        34.92        11.97         6.21         1.12         3.75 
TCGA-14-1402 TCGA-14-1794 TCGA-14-1795 TCGA-14-2555 TCGA-19-2625 TCGA-19-4068 
       32.05         0.99         1.97         7.96         4.08         4.50 
TCGA-26-1443 TCGA-26-5132 TCGA-27-1830 TCGA-27-1838 TCGA-27-2524 TCGA-28-1750 
        7.13         9.40         5.06        11.51         7.59         8.35 
TCGA-28-1753 TCGA-28-1755 TCGA-28-1757 TCGA-28-1760 TCGA-32-1977 TCGA-32-1978 
        1.22         1.55         0.13         4.70         0.10        15.85 
TCGA-32-1982 TCGA-32-1986 TCGA-32-2491 TCGA-32-2494 TCGA-32-2615 TCGA-32-4719 
        4.67        12.69        12.23        20.78        15.95        10.85 
TCGA-41-2571 TCGA-41-2572 TCGA-41-6646 TCGA-74-6581 TCGA-76-4928 TCGA-76-6661 
        0.85        13.35        12.46         8.22         3.09        23.90 
TCGA-76-6664 TCGA-02-0021 TCGA-02-0025 TCGA-02-0028 TCGA-02-0034 TCGA-02-0047 
       36.20        77.65        42.74        90.58        14.14        14.73 
TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 TCGA-02-0106 TCGA-02-0107 
       19.73        26.43        25.05         5.49        11.67        17.65 
TCGA-02-0111 TCGA-02-0113 TCGA-02-0266 TCGA-02-0285 TCGA-02-0317 TCGA-02-0332 
       23.18        92.65        17.72        13.87        12.23        25.71 
TCGA-02-0333 TCGA-02-0337 TCGA-02-0432 TCGA-02-0456 TCGA-06-0124 TCGA-06-0127 
        4.37        25.12        47.11         3.35        20.38         3.98 
TCGA-06-0130 TCGA-06-0133 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 TCGA-06-0143 
       12.95        14.30        11.90         0.20        10.29        11.74 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0156 
        8.61        19.46        12.33        13.94        10.45         5.85 
TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 TCGA-06-0169 TCGA-06-0175 TCGA-06-0188 
       56.91         5.85        19.66         3.29         4.04        44.58 
TCGA-06-0189 TCGA-06-0210 TCGA-06-0238 TCGA-06-0409 TCGA-06-0645 TCGA-06-0650 
       15.42         7.40        13.32        72.36         5.75        23.57 
TCGA-06-0743 TCGA-06-0744 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-1084 
       26.40        46.88        46.19         7.17        16.57        23.93 
TCGA-06-1086 TCGA-06-1802 TCGA-06-1805 TCGA-06-2563 TCGA-06-2569 TCGA-06-6693 
        6.84        15.32        33.90        30.64         0.43       120.56 
TCGA-08-0353 TCGA-08-0356 TCGA-08-0358 TCGA-08-0373 TCGA-08-0392 TCGA-08-0524 
        8.42        31.10        22.29         4.41         0.72         7.27 
TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0688 TCGA-12-0703 
       14.73        10.45         7.59        94.78        26.66        20.38 
TCGA-12-0778 TCGA-12-1093 TCGA-12-1096 TCGA-14-0813 TCGA-14-0871 TCGA-15-1447 
       14.93        15.98         9.11         1.35        28.93        53.19 
TCGA-19-0957 TCGA-26-6173 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 
       21.90         7.92        11.77        31.27        23.44        13.64 
TCGA-28-5218 TCGA-76-6280 TCGA-81-5910 
        5.16        11.38         1.61 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     0.39     0.10 
subtype1 subtype2 subtype3 subtype4 
   91.00   127.59    65.33   120.56 
subtype1 subtype2 subtype3 subtype4 
  12.100   12.990    9.635   12.460 
[1] "0.1 - 91.0 (12.1)"  "0.1 - 127.6 (13.0)" "0.4 - 65.3 (9.6)"  
[4] "0.1 - 120.6 (12.5)"
D3V2, continuous
D3V3, binary
          cls
clus         0
  subtype1 151
  subtype2 189
  subtype3  93
  subtype4 130
[1] "NOT AVAILABLE: table only has an event [0]"
D3V4, binary
          cls
clus         0   1
  subtype1  59  92
  subtype2  80 109
  subtype3  36  57
  subtype4  44  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   92
  subtype2   80  109
  subtype3   36   57
  subtype4   44   86
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       59       80       36       44
  MALE         92      109       57       86
[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"
D3V5, binary
          cls
clus         0   1
  subtype1  17 129
  subtype2  22 157
  subtype3  18  72
  subtype4  16 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  129
  subtype2   22  157
  subtype3   18   72
  subtype4   16  108
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        17       22       18       16
  YES      129      157       72      108
[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"
D3V6, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             2                   3
  subtype2                             3                   9
  subtype3                             3                   5
  subtype4                             3                   3
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             146
  subtype2                             177
  subtype3                              85
  subtype4                             124
D3V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  GLIOBLASTOMA MULTIFORME (GBM)          2        3        3        3
  TREATED PRIMARY GBM                    3        9        5        3
  UNTREATED PRIMARY (DE NOVO) GBM      146      177       85      124
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        13   127
  subtype2     7                         9   162
  subtype3     1                         1    89
  subtype4     2                         7   117
D3V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        7        1        2
  BLACK OR AFRICAN AMERICAN       13        9        1        7
  WHITE                          127      162       89      117
[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"
D3V9, binary
          cls
clus         0   1
  subtype1   3 124
  subtype2   4 158
  subtype3   2  74
  subtype4   3 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  124
  subtype2    4  158
  subtype3    2   74
  subtype4    3  105
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        4        2        3
  NOT HISPANIC OR LATINO      124      158       74      105
[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(4) Variable = MIR_CHIERARCHICAL
D4V1, survival
          sevent
clus2        0   1
  subtype1  47 255
  subtype2  22 106
  subtype3  23 108
subtype1 subtype2 subtype3 
     302      128      131 
subtype1 subtype2 subtype3 
     255      106      108 
$subtype1
TCGA-06-6391 TCGA-06-5410 TCGA-06-5411 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 
        1.48         3.55         8.35         8.55         6.71         5.10 
TCGA-06-5856 TCGA-06-6388 TCGA-06-6700 TCGA-06-6701 TCGA-12-1092 TCGA-12-1597 
        3.75         5.23         4.77         4.96        21.73        22.19 
TCGA-12-1598 TCGA-12-1599 TCGA-12-3644 TCGA-12-3646 TCGA-12-3649 TCGA-12-3650 
       15.65        25.68        59.77        44.02        15.22        10.95 
TCGA-12-3651 TCGA-12-5299 TCGA-12-5301 TCGA-14-0740 TCGA-14-0812 TCGA-14-0865 
       12.69         3.22         2.04        11.97         3.25        16.50 
TCGA-14-0866 TCGA-14-1401 TCGA-14-1451 TCGA-14-1454 TCGA-14-1455 TCGA-14-1456 
       26.33         3.75        23.11        30.18         0.92        40.96 
TCGA-14-1458 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 TCGA-14-1821 TCGA-14-1825 
        6.67        12.43         0.99         1.97        17.79         7.63 
TCGA-14-1827 TCGA-14-1829 TCGA-14-3476 TCGA-14-3477 TCGA-14-4157 TCGA-16-1045 
        5.88         7.17         0.39         3.78         3.42        29.03 
TCGA-16-1055 TCGA-16-1060 TCGA-16-1063 TCGA-16-1460 TCGA-19-0960 TCGA-19-0963 
       10.29         9.14        13.97         6.41         8.61        14.27 
TCGA-19-1390 TCGA-19-1392 TCGA-19-1788 TCGA-19-1791 TCGA-19-2620 TCGA-19-2624 
       25.38         3.65         3.68         0.13         4.87         0.16 
TCGA-19-4068 TCGA-19-5950 TCGA-19-5955 TCGA-19-5956 TCGA-19-5960 TCGA-26-1799 
        4.50        17.19         1.78        22.49        14.96         9.37 
TCGA-26-5135 TCGA-26-5136 TCGA-27-1836 TCGA-27-1837 TCGA-27-2518 TCGA-27-2519 
        8.88        18.97        30.05        14.04        24.76        18.08 
TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2527 TCGA-28-1746 TCGA-28-1747 
       16.77        16.08         7.59        14.40         0.20         2.53 
TCGA-28-1752 TCGA-28-1756 TCGA-28-2502 TCGA-28-2506 TCGA-32-1970 TCGA-32-1973 
        8.48         2.83         0.66         6.74        15.39        21.07 
TCGA-32-1976 TCGA-32-1980 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 
        0.49         1.18        16.93        12.23        20.78        15.02 
TCGA-32-2634 TCGA-32-4208 TCGA-32-4210 TCGA-32-4719 TCGA-41-2571 TCGA-41-2572 
       22.78        21.14         3.72        10.85         0.85        13.35 
TCGA-41-2573 TCGA-41-3392 TCGA-41-3915 TCGA-41-5651 TCGA-41-6646 TCGA-74-6581 
        8.94         0.99        11.84        15.12        12.46         8.22 
TCGA-74-6584 TCGA-76-4926 TCGA-76-4927 TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 
        7.50         4.54        17.59         2.53        36.85        16.70 
TCGA-76-6192 TCGA-76-6662 TCGA-76-6663 TCGA-02-0001 TCGA-02-0003 TCGA-02-0007 
        3.29        34.45        18.64        11.77         4.73        23.18 
TCGA-02-0010 TCGA-02-0011 TCGA-02-0014 TCGA-02-0015 TCGA-02-0016 TCGA-02-0023 
       35.41        20.71        82.59        20.61        87.06        20.12 
TCGA-02-0024 TCGA-02-0026 TCGA-02-0027 TCGA-02-0028 TCGA-02-0038 TCGA-02-0039 
       53.10        24.59        12.16        90.58        10.72        10.52 
TCGA-02-0047 TCGA-02-0048 TCGA-02-0052 TCGA-02-0057 TCGA-02-0058 TCGA-02-0060 
       14.73         3.22        12.59        19.86         8.35         6.02 
TCGA-02-0069 TCGA-02-0071 TCGA-02-0074 TCGA-02-0079 TCGA-02-0080 TCGA-02-0084 
       28.70         5.49        10.19        27.25        89.72        12.62 
TCGA-02-0085 TCGA-02-0087 TCGA-02-0089 TCGA-02-0104 TCGA-02-0114 TCGA-02-0115 
       51.32        57.76        16.96        65.00        99.98        15.65 
TCGA-02-0116 TCGA-02-0258 TCGA-02-0266 TCGA-02-0281 TCGA-02-0321 TCGA-02-0325 
       48.95        16.54        17.72         3.98         9.90        10.62 
TCGA-02-0326 TCGA-02-0330 TCGA-02-0332 TCGA-02-0337 TCGA-02-0339 TCGA-02-0432 
        7.33        15.91        25.71        25.12        12.39        47.11 
TCGA-02-0439 TCGA-02-0440 TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 
        0.66        11.34         9.27        16.21        16.80        12.92 
TCGA-02-2483 TCGA-06-0122 TCGA-06-0126 TCGA-06-0127 TCGA-06-0128 TCGA-06-0129 
       15.32         6.15         6.94         3.98        22.72        33.67 
TCGA-06-0133 TCGA-06-0138 TCGA-06-0142 TCGA-06-0143 TCGA-06-0146 TCGA-06-0147 
       14.30        24.23         2.20        11.74        20.09        17.79 
TCGA-06-0150 TCGA-06-0156 TCGA-06-0158 TCGA-06-0159 TCGA-06-0160 TCGA-06-0162 
       19.46         5.85        10.82         9.44        11.80         3.42 
TCGA-06-0166 TCGA-06-0168 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 
        5.85        19.66        13.12         4.47         3.22         4.04 
TCGA-06-0177 TCGA-06-0178 TCGA-06-0179 TCGA-06-0184 TCGA-06-0185 TCGA-06-0188 
        4.18        88.14        20.25        69.90        73.84        44.58 
TCGA-06-0195 TCGA-06-0208 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 TCGA-06-0219 
        7.40         8.42         0.53        15.02        24.16         0.72 
TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0240 TCGA-06-0241 TCGA-06-0410 
       19.82        13.64        13.32        20.42        48.69         4.70 
TCGA-06-0413 TCGA-06-0414 TCGA-06-0646 TCGA-06-0648 TCGA-06-0650 TCGA-06-0686 
        3.16        35.11         5.75         9.80        23.57        14.20 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0750 TCGA-06-0875 TCGA-06-0882 
       46.88         7.86         2.70         0.92        43.46        20.78 
TCGA-06-0939 TCGA-06-1087 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 TCGA-06-1805 
       26.76         4.04        11.84        15.32        13.61        33.90 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2566 TCGA-06-2570 TCGA-06-6389 TCGA-06-6693 TCGA-08-0244 TCGA-08-0245 
        5.98        31.50         7.79       120.56        22.68        37.84 
TCGA-08-0344 TCGA-08-0345 TCGA-08-0347 TCGA-08-0348 TCGA-08-0349 TCGA-08-0350 
      115.86         1.74        25.71        12.16         9.80        29.23 
TCGA-08-0351 TCGA-08-0352 TCGA-08-0357 TCGA-08-0359 TCGA-08-0373 TCGA-08-0375 
       65.33         1.28        37.58         3.39         4.41        12.23 
TCGA-08-0380 TCGA-08-0385 TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 
       14.93         2.70        18.02        15.35        13.97        12.56 
TCGA-08-0511 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 TCGA-08-0524 TCGA-12-0618 
        7.73        19.59        58.68         4.80         7.27        12.99 
TCGA-12-0656 TCGA-12-0670 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 TCGA-12-0707 
       94.78        25.97        12.13         3.65        20.38        28.41 
TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0780 TCGA-12-0820 TCGA-12-0821 
       15.06        53.85        43.23        14.86        18.48        10.62 
TCGA-12-0822 TCGA-12-0827 TCGA-12-1089 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       23.51        38.76         5.82        15.85         9.11        14.53 
TCGA-12-1099 TCGA-14-0813 TCGA-14-0867 TCGA-14-1043 TCGA-15-1444 TCGA-15-1446 
        4.14         1.35         2.04         0.79        50.53        19.10 
TCGA-15-1447 TCGA-15-1449 TCGA-16-0846 TCGA-16-0849 TCGA-16-0850 TCGA-19-0955 
       53.19        13.28         3.91        26.07        16.37        11.77 
TCGA-19-0957 TCGA-19-0962 TCGA-19-1387 TCGA-19-1388 TCGA-19-1389 TCGA-26-1442 
       21.90         0.66         5.95        12.95         4.64        31.33 
TCGA-26-5133 TCGA-26-5134 TCGA-26-5139 TCGA-26-6174 TCGA-28-2514 TCGA-28-5207 
       14.86         5.49         1.58         2.33         5.26        11.28 
TCGA-28-5213 TCGA-28-5214 TCGA-28-5216 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 
       31.27        23.44        13.64        22.68        12.76         5.42 
TCGA-32-2616 TCGA-76-6283 
        7.36         5.42 

$subtype2
TCGA-06-1806 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5418 TCGA-12-1602 
       15.32         4.54         8.81         8.98         2.73         6.77 
TCGA-12-5295 TCGA-14-0781 TCGA-14-0862 TCGA-14-1034 TCGA-14-1396 TCGA-14-1402 
       14.93         0.95         2.89        15.95         1.12        32.05 
TCGA-14-2555 TCGA-19-0964 TCGA-19-1790 TCGA-19-2625 TCGA-19-5947 TCGA-19-5952 
        7.96         3.39         5.06         4.08         6.64        18.90 
TCGA-26-1439 TCGA-26-1443 TCGA-26-5132 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
       13.87         7.13         9.40         5.06        16.60         9.86 
TCGA-27-1838 TCGA-27-2528 TCGA-28-1745 TCGA-28-1751 TCGA-28-1753 TCGA-28-1755 
       11.51        15.78        11.34         7.63         1.22         1.55 
TCGA-28-1757 TCGA-28-1760 TCGA-32-1977 TCGA-32-1978 TCGA-32-1982 TCGA-32-1986 
        0.13         4.70         0.10        15.85         4.67        12.69 
TCGA-32-2615 TCGA-32-2632 TCGA-32-2638 TCGA-76-4928 TCGA-76-6661 TCGA-76-6664 
       15.95         8.84        25.18         3.09        23.90        36.20 
TCGA-02-0004 TCGA-02-0006 TCGA-02-0021 TCGA-02-0025 TCGA-02-0033 TCGA-02-0034 
       11.34        18.35        77.65        42.74         2.83        14.14 
TCGA-02-0037 TCGA-02-0051 TCGA-02-0055 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 
        3.62        15.09         2.50         9.57        19.73        26.43 
TCGA-02-0070 TCGA-02-0086 TCGA-02-0106 TCGA-02-0107 TCGA-02-0111 TCGA-02-0113 
       25.05         8.81        11.67        17.65        23.18        92.65 
TCGA-02-0285 TCGA-02-0290 TCGA-02-0317 TCGA-02-0333 TCGA-02-0338 TCGA-02-0456 
       13.87        15.95        12.23         4.37        10.59         3.35 
TCGA-02-2486 TCGA-06-0124 TCGA-06-0130 TCGA-06-0139 TCGA-06-0140 TCGA-06-0141 
       20.32        20.38        12.95        11.90         0.20        10.29 
TCGA-06-0149 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 TCGA-06-0164 
        8.61        46.59        12.33        13.94        10.45        56.91 
TCGA-06-0169 TCGA-06-0176 TCGA-06-0189 TCGA-06-0190 TCGA-06-0194 TCGA-06-0197 
        3.29        91.00        15.42        10.42         4.67         5.56 
TCGA-06-0210 TCGA-06-0394 TCGA-06-0397 TCGA-06-0409 TCGA-06-0412 TCGA-06-0644 
        7.40        10.82         9.01        72.36         9.57        12.62 
TCGA-06-0645 TCGA-06-0743 TCGA-06-0876 TCGA-06-0878 TCGA-06-0881 TCGA-06-1084 
        5.75        26.40        46.19         7.17        16.57        23.93 
TCGA-06-1086 TCGA-06-1800 TCGA-06-2569 TCGA-06-6694 TCGA-08-0246 TCGA-08-0346 
        6.84        26.79         0.43         7.36         4.18         8.42 
TCGA-08-0353 TCGA-08-0354 TCGA-08-0356 TCGA-08-0358 TCGA-08-0392 TCGA-08-0512 
        8.42        17.95        31.10        22.29         0.72        42.15 
TCGA-08-0522 TCGA-12-0616 TCGA-12-0620 TCGA-12-0654 TCGA-12-0776 TCGA-12-0778 
       20.88        14.73        10.45         7.59         9.73        14.93 
TCGA-12-0828 TCGA-12-0829 TCGA-12-1093 TCGA-12-1094 TCGA-14-0789 TCGA-14-0871 
        8.94        20.58        15.98        12.23        11.24        28.93 
TCGA-14-1037 TCGA-19-1385 TCGA-26-6173 TCGA-28-2513 TCGA-28-5211 TCGA-28-5218 
       19.30        10.75         7.92         7.30        11.77         5.16 
TCGA-76-6280 TCGA-81-5910 
       11.38         1.61 

$subtype3
TCGA-06-5408 TCGA-06-5858 TCGA-06-5859 TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 
       11.74         6.15         4.57         8.32        12.85         4.77 
TCGA-06-6699 TCGA-12-1600 TCGA-12-3648 TCGA-12-3652 TCGA-12-3653 TCGA-14-0736 
        1.55        14.73        26.93        34.92        14.53        15.12 
TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 TCGA-14-1395 TCGA-14-1450 TCGA-14-1452 
        6.21        23.05        13.78         1.38        58.78         7.10 
TCGA-14-1453 TCGA-14-1823 TCGA-14-2554 TCGA-16-0848 TCGA-16-1047 TCGA-16-1056 
        1.15        17.85        17.49        17.59         4.57        14.01 
TCGA-16-1062 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-2619 TCGA-19-2621 
       21.24         7.17        12.66         3.25         9.67         1.08 
TCGA-19-2623 TCGA-19-2629 TCGA-19-2631 TCGA-19-5951 TCGA-19-5953 TCGA-19-5954 
        7.53        24.23         7.00         8.02         4.73        12.10 
TCGA-19-5958 TCGA-19-5959 TCGA-26-1438 TCGA-26-1440 TCGA-27-1833 TCGA-27-1834 
       14.07        16.80        10.03         9.73        24.23        40.54 
TCGA-27-1835 TCGA-27-2526 TCGA-28-1749 TCGA-28-1750 TCGA-28-2509 TCGA-32-1979 
       21.30         2.86         9.21         8.35         4.77        19.50 
TCGA-32-1987 TCGA-32-4209 TCGA-32-4211 TCGA-32-4213 TCGA-32-5222 TCGA-41-2575 
       14.86        20.32        12.59        19.86        19.23         9.53 
TCGA-41-3393 TCGA-41-4097 TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 
        4.44         0.20         3.45        20.91         4.34        14.33 
TCGA-76-4925 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-76-6193 TCGA-76-6282 
        4.80         3.65         9.17        47.93         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-02-0009 TCGA-02-0043 
        8.35        20.98         4.83         5.03        10.59        18.31 
TCGA-02-0054 TCGA-02-0075 TCGA-02-0083 TCGA-02-0099 TCGA-02-0102 TCGA-02-0260 
        6.54        20.84        22.72         3.48        27.02        16.93 
TCGA-02-0269 TCGA-02-0271 TCGA-02-0289 TCGA-02-0324 TCGA-02-0422 TCGA-02-0430 
       10.75        14.47        14.20         7.73        14.50        10.55 
TCGA-02-2485 TCGA-06-0125 TCGA-06-0137 TCGA-06-0145 TCGA-06-0157 TCGA-06-0182 
       15.45        47.61        26.70         2.33         3.19         3.65 
TCGA-06-0187 TCGA-06-0192 TCGA-06-0211 TCGA-06-0402 TCGA-06-0649 TCGA-06-0749 
       27.22        38.96        11.84         0.26         2.10         2.70 
TCGA-06-0879 TCGA-06-2557 TCGA-06-2565 TCGA-06-2567 TCGA-06-6390 TCGA-08-0355 
       40.41         1.08        16.64         4.37         5.39        24.56 
TCGA-08-0360 TCGA-08-0510 TCGA-08-0514 TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 
       15.39         4.27        11.08        19.33        10.75        15.98 
TCGA-08-0529 TCGA-08-0531 TCGA-12-0619 TCGA-12-0657 TCGA-12-0662 TCGA-12-0688 
       18.41         7.56        34.92         0.10        38.17        26.66 
TCGA-12-0775 TCGA-12-0826 TCGA-12-1088 TCGA-12-1090 TCGA-12-1091 TCGA-12-1098 
        7.63        27.78       127.59         7.59        33.21         3.98 
TCGA-14-0787 TCGA-14-0817 TCGA-15-0742 TCGA-19-1386 TCGA-28-5204 TCGA-28-5208 
        2.24         5.39        13.78         9.07        14.93        17.88 
TCGA-28-5209 TCGA-28-5215 TCGA-76-6660 TCGA-81-5911 TCGA-87-5896 
       14.53        11.01         3.75        17.72        26.30 

subtype1 subtype2 subtype3 
    0.13     0.10     0.10 
subtype1 subtype2 subtype3 
  120.56    92.65   127.59 
subtype1 subtype2 subtype3 
  12.725   11.030   11.840 
[1] "0.1 - 120.6 (12.7)" "0.1 - 92.7 (11.0)"  "0.1 - 127.6 (11.8)"
D4V2, continuous
D4V3, binary
          cls
clus         0
  subtype1 303
  subtype2 129
  subtype3 131
[1] "NOT AVAILABLE: table only has an event [0]"
D4V4, binary
          cls
clus         0   1
  subtype1 111 192
  subtype2  48  81
  subtype3  60  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111  192
  subtype2   48   81
  subtype3   60   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      111       48       60
  MALE        192       81       71
[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"
D4V5, binary
          cls
clus         0   1
  subtype1  44 246
  subtype2  13 109
  subtype3  16 111
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44  246
  subtype2   13  109
  subtype3   16  111
     clus
vv    subtype1 subtype2 subtype3
  NO        44       13       16
  YES      246      109      111
[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"
D4V6, continuous
          vv
clus       GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM
  subtype1                             7                  13
  subtype2                             3                   2
  subtype3                             1                   5
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             283
  subtype2                             124
  subtype3                             125
D4V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  GLIOBLASTOMA MULTIFORME (GBM)          7        3        1
  TREATED PRIMARY GBM                   13        2        5
  UNTREATED PRIMARY (DE NOVO) GBM      283      124      125
[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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                        10   273
  subtype2     3                        11   113
  subtype3     3                         9   109
D4V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            7        3        3
  BLACK OR AFRICAN AMERICAN       10       11        9
  WHITE                          273      113      109
[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"
D4V9, binary
          cls
clus         0   1
  subtype1   6 250
  subtype2   2 109
  subtype3   4 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  250
  subtype2    2  109
  subtype3    4  102
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        2        4
  NOT HISPANIC OR LATINO      250      109      102
[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(5) Variable = CN_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  93 433
  subtype2 350 114
  subtype3  37  51
subtype1 subtype2 subtype3 
     526      464       88 
subtype1 subtype2 subtype3 
     433      114       51 
$subtype1
TCGA-E1-A7YN TCGA-06-1806 TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 
       23.90        15.32        11.74         8.35         8.81         8.98 
TCGA-06-5415 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        8.55         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U1 
        8.32        12.85         4.77         1.55         4.77         1.87 
TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-0615 TCGA-12-1092 TCGA-12-1598 
        3.12         2.56        14.60        15.35        21.73        15.65 
TCGA-12-1599 TCGA-12-1600 TCGA-12-1602 TCGA-12-3644 TCGA-12-3646 TCGA-12-3648 
       25.68        14.73         6.77        59.77        44.02        26.93 
TCGA-12-3649 TCGA-12-3650 TCGA-12-3651 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       15.22        10.95        12.69        34.92        14.53        14.93 
TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 TCGA-14-0783 TCGA-14-0786 TCGA-14-0790 
        3.22         2.04        15.12         6.21        23.05        13.78 
TCGA-14-0812 TCGA-14-0862 TCGA-14-0865 TCGA-14-0866 TCGA-14-1034 TCGA-14-1395 
        3.25         2.89        16.50        26.33        15.95         1.38 
TCGA-14-1396 TCGA-14-1401 TCGA-14-1402 TCGA-14-1450 TCGA-14-1451 TCGA-14-1452 
        1.12         3.75        32.05        58.78        23.11         7.10 
TCGA-14-1453 TCGA-14-1454 TCGA-14-1455 TCGA-14-1459 TCGA-14-1794 TCGA-14-1795 
        1.15        30.18         0.92        12.43         0.99         1.97 
TCGA-14-1823 TCGA-14-1825 TCGA-14-1827 TCGA-14-1829 TCGA-14-2554 TCGA-14-2555 
       17.85         7.63         5.88         7.17        17.49         7.96 
TCGA-14-4157 TCGA-16-0848 TCGA-16-1045 TCGA-16-1047 TCGA-16-1055 TCGA-16-1056 
        3.42        17.59        29.03         4.57        10.29        14.01 
TCGA-16-1060 TCGA-16-1062 TCGA-16-1063 TCGA-19-0963 TCGA-19-0964 TCGA-19-1390 
        9.14        21.24        13.97        14.27         3.39        25.38 
TCGA-19-1392 TCGA-19-1786 TCGA-19-1787 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
        3.65         7.17        12.66         3.25         0.13         9.67 
TCGA-19-2620 TCGA-19-2621 TCGA-19-2624 TCGA-19-2629 TCGA-19-2631 TCGA-19-4065 
        4.87         1.08         0.16        24.23         7.00         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 
        1.78        14.07        16.80        14.96        17.79        28.54 
TCGA-26-1438 TCGA-26-1439 TCGA-26-1440 TCGA-26-1443 TCGA-26-1799 TCGA-26-5132 
       10.03        13.87         9.73         7.13         9.37         9.40 
TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 
        8.88        18.97        19.33         5.06        16.60         9.86 
TCGA-27-1833 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 TCGA-27-1838 TCGA-27-2518 
       24.23        40.54        21.30        14.04        11.51        24.76 
TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 TCGA-28-1746 
       18.08        16.08         7.59         2.86        15.78         0.20 
TCGA-28-1747 TCGA-28-1749 TCGA-28-1750 TCGA-28-1751 TCGA-28-1752 TCGA-28-1753 
        2.53         9.21         8.35         7.63         8.48         1.22 
TCGA-28-1755 TCGA-28-1757 TCGA-28-2502 TCGA-28-2506 TCGA-28-2509 TCGA-32-1970 
        1.55         0.13         0.66         6.74         4.77        15.39 
TCGA-32-1976 TCGA-32-1977 TCGA-32-1978 TCGA-32-1979 TCGA-32-1982 TCGA-32-1986 
        0.49         0.10        15.85        19.50         4.67        12.69 
TCGA-32-1987 TCGA-32-1991 TCGA-32-2491 TCGA-32-2494 TCGA-32-2495 TCGA-32-2615 
       14.86        16.93        12.23        20.78        15.02        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4210 TCGA-32-4211 TCGA-32-4213 
        8.84        22.78        25.18         3.72        12.59        19.86 
TCGA-32-4719 TCGA-32-5222 TCGA-41-2571 TCGA-41-2572 TCGA-41-2573 TCGA-41-2575 
       10.85        19.23         0.85        13.35         8.94         9.53 
TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S 
        0.99         4.44        15.12        12.46         4.08         1.45 
TCGA-4W-AA9T TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 
       25.58         3.45        20.91         4.34        14.33         8.22 
TCGA-74-6584 TCGA-76-4925 TCGA-76-4926 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 
        7.50         4.80         4.54         3.09         3.65         9.17 
TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6282 TCGA-76-6285 TCGA-76-6286 
       36.85        16.70         3.29        17.06         8.35        20.98 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 TCGA-76-6663 TCGA-76-6664 
        4.83         5.03        23.90        34.45        18.64        36.20 
TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-CS-4941 TCGA-CS-5395 TCGA-CS-5397 
        5.92         6.28        20.55         7.69        21.01         6.38 
TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-A4X9 TCGA-DB-A64O TCGA-DH-A669 TCGA-DU-5852 
       17.69        26.76        46.42        25.48        30.21         6.74 
TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 
        8.45       211.17        49.02         7.04        11.64       133.74 
TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 
       19.89        16.83        94.52        11.47         6.54         8.84 
TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-A5TT TCGA-DU-A5TY 
       10.36         7.96         5.10        23.74        24.43        33.96 
TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-A7YD 
       11.41        26.76        84.33         7.50         0.56        14.30 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YM TCGA-E1-A7YQ TCGA-E1-A7Z2 TCGA-FG-6692 
       19.46        16.18        21.30        51.88        13.08        18.44 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7860 TCGA-HT-8011 
       10.72        18.38        10.78         5.72         0.49        16.24 
TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 
       12.23        13.78         0.23        27.35         5.33        16.14 
TCGA-HT-A61C TCGA-KT-A7W1 TCGA-P5-A72U TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6U0 
       17.65        14.40         0.23        14.53        16.70        24.39 
TCGA-S9-A6WM TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84B 
       19.86        26.93        19.99        10.39        54.77        24.92 
TCGA-TQ-A7RM TCGA-VM-A8CD TCGA-VW-A8FI TCGA-06-0209 TCGA-02-0001 TCGA-02-0003 
       36.69         7.89         8.05         7.63        11.77         4.73 
TCGA-02-0006 TCGA-02-0007 TCGA-02-0009 TCGA-02-0010 TCGA-02-0015 TCGA-02-0016 
       18.35        23.18        10.59        35.41        20.61        87.06 
TCGA-02-0021 TCGA-02-0023 TCGA-02-0024 TCGA-02-0025 TCGA-02-0027 TCGA-02-0034 
       77.65        20.12        53.10        42.74        12.16        14.14 
TCGA-02-0037 TCGA-02-0038 TCGA-02-0043 TCGA-02-0046 TCGA-02-0048 TCGA-02-0051 
        3.62        10.72        18.31         6.87         3.22        15.09 
TCGA-02-0054 TCGA-02-0059 TCGA-02-0064 TCGA-02-0068 TCGA-02-0070 TCGA-02-0071 
        6.54         9.57        19.73        26.43        25.05         5.49 
TCGA-02-0074 TCGA-02-0075 TCGA-02-0079 TCGA-02-0083 TCGA-02-0086 TCGA-02-0089 
       10.19        20.84        27.25        22.72         8.81        16.96 
TCGA-02-0099 TCGA-02-0102 TCGA-02-0106 TCGA-02-0115 TCGA-02-0116 TCGA-02-0258 
        3.48        27.02        11.67        15.65        48.95        16.54 
TCGA-02-0260 TCGA-02-0266 TCGA-02-0269 TCGA-02-0271 TCGA-02-0281 TCGA-02-0285 
       16.93        17.72        10.75        14.47         3.98        13.87 
TCGA-02-0289 TCGA-02-0290 TCGA-02-0317 TCGA-02-0321 TCGA-02-0324 TCGA-02-0325 
       14.20        15.95        12.23         9.90         7.73        10.62 
TCGA-02-0330 TCGA-02-0333 TCGA-02-0337 TCGA-02-0422 TCGA-02-0430 TCGA-02-0440 
       15.91         4.37        25.12        14.50        10.55        11.34 
TCGA-02-0446 TCGA-02-0451 TCGA-02-2466 TCGA-02-2470 TCGA-02-2485 TCGA-02-2486 
        9.27        16.21        16.80        12.92        15.45        20.32 
TCGA-06-0122 TCGA-06-0124 TCGA-06-0125 TCGA-06-0126 TCGA-06-0130 TCGA-06-0133 
        6.15        20.38        47.61         6.94        12.95        14.30 
TCGA-06-0137 TCGA-06-0138 TCGA-06-0140 TCGA-06-0143 TCGA-06-0145 TCGA-06-0148 
       26.70        24.23         0.20        11.74         2.33        10.09 
TCGA-06-0149 TCGA-06-0150 TCGA-06-0151 TCGA-06-0152 TCGA-06-0154 TCGA-06-0155 
        8.61        19.46        46.59        12.33        13.94        10.45 
TCGA-06-0157 TCGA-06-0158 TCGA-06-0162 TCGA-06-0164 TCGA-06-0166 TCGA-06-0168 
        3.19        10.82         3.42        56.91         5.85        19.66 
TCGA-06-0169 TCGA-06-0171 TCGA-06-0173 TCGA-06-0174 TCGA-06-0175 TCGA-06-0177 
        3.29        13.12         4.47         3.22         4.04         4.18 
TCGA-06-0182 TCGA-06-0184 TCGA-06-0185 TCGA-06-0187 TCGA-06-0188 TCGA-06-0190 
        3.65        69.90        73.84        27.22        44.58        10.42 
TCGA-06-0192 TCGA-06-0194 TCGA-06-0195 TCGA-06-0197 TCGA-06-0201 TCGA-06-0206 
       38.96         4.67         7.40         5.56         0.39         7.66 
TCGA-06-0208 TCGA-06-0210 TCGA-06-0211 TCGA-06-0213 TCGA-06-0214 TCGA-06-0216 
        8.42         7.40        11.84         0.53        15.02        24.16 
TCGA-06-0219 TCGA-06-0221 TCGA-06-0237 TCGA-06-0238 TCGA-06-0241 TCGA-06-0394 
        0.72        19.82        13.64        13.32        48.69        10.82 
TCGA-06-0397 TCGA-06-0402 TCGA-06-0409 TCGA-06-0412 TCGA-06-0413 TCGA-06-0644 
        9.01         0.26        72.36         9.57         3.16        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0648 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 
        5.75         5.75         9.80         2.10        14.20        26.40 
TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0875 
       46.88         7.86         2.70         2.70         0.92        43.46 
TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-0882 TCGA-06-0939 TCGA-06-1084 
       46.19         7.17        40.41        20.78        26.76        23.93 
TCGA-06-1086 TCGA-06-1087 TCGA-06-1800 TCGA-06-1801 TCGA-06-1802 TCGA-06-1804 
        6.84         4.04        26.79        11.84        15.32        13.61 
TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 
        1.08        12.49         4.93        17.65        12.56        30.64 
TCGA-06-2564 TCGA-06-2565 TCGA-06-2566 TCGA-06-2567 TCGA-06-6390 TCGA-06-6693 
        5.95        16.64         5.98         4.37         5.39       120.56 
TCGA-06-6694 TCGA-08-0244 TCGA-08-0246 TCGA-08-0345 TCGA-08-0346 TCGA-08-0347 
        7.36        22.68         4.18         1.74         8.42        25.71 
TCGA-08-0348 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0355 
       12.16         9.80         1.28         8.42        17.95        24.56 
TCGA-08-0356 TCGA-08-0357 TCGA-08-0358 TCGA-08-0359 TCGA-08-0375 TCGA-08-0380 
       31.10        37.58        22.29         3.39        12.23        14.93 
TCGA-08-0386 TCGA-08-0389 TCGA-08-0390 TCGA-08-0509 TCGA-08-0510 TCGA-08-0514 
       18.02        15.35        13.97        12.56         4.27        11.08 
TCGA-08-0518 TCGA-08-0520 TCGA-08-0525 TCGA-08-0529 TCGA-08-0531 TCGA-12-0616 
       19.33        10.75        15.98        18.41         7.56        14.73 
TCGA-12-0618 TCGA-12-0619 TCGA-12-0620 TCGA-12-0654 TCGA-12-0656 TCGA-12-0657 
       12.99        34.92        10.45         7.59        94.78         0.10 
TCGA-12-0662 TCGA-12-0670 TCGA-12-0688 TCGA-12-0691 TCGA-12-0692 TCGA-12-0703 
       38.17        25.97        26.66        12.13         3.65        20.38 
TCGA-12-0707 TCGA-12-0769 TCGA-12-0772 TCGA-12-0773 TCGA-12-0775 TCGA-12-0776 
       28.41        15.06        53.85        43.23         7.63         9.73 
TCGA-12-0778 TCGA-12-0780 TCGA-12-0819 TCGA-12-0820 TCGA-12-0821 TCGA-12-0822 
       14.93        14.86        24.79        18.48        10.62        23.51 
TCGA-12-0826 TCGA-12-0828 TCGA-12-0829 TCGA-12-1088 TCGA-12-1089 TCGA-12-1090 
       27.78         8.94        20.58       127.59         5.82         7.59 
TCGA-12-1091 TCGA-12-1093 TCGA-12-1094 TCGA-12-1095 TCGA-12-1096 TCGA-12-1097 
       33.21        15.98        12.23        15.85         9.11        14.53 
TCGA-12-1098 TCGA-12-1099 TCGA-14-0787 TCGA-14-0789 TCGA-14-0813 TCGA-14-0817 
        3.98         4.14         2.24        11.24         1.35         5.39 
TCGA-14-1037 TCGA-14-1043 TCGA-15-0742 TCGA-15-1446 TCGA-15-1449 TCGA-16-0846 
       19.30         0.79        13.78        19.10        13.28         3.91 
TCGA-19-0955 TCGA-19-0957 TCGA-19-0962 TCGA-19-1386 TCGA-19-1387 TCGA-19-1388 
       11.77        21.90         0.66         9.07         5.95        12.95 
TCGA-26-5134 TCGA-26-5139 TCGA-26-6173 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        5.49         1.58         7.92         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5218 
       17.88        14.53        11.77        31.27        23.44         5.16 
TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-32-2616 TCGA-76-6280 TCGA-76-6283 
       22.68        12.76         5.42         7.36        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

$subtype2
TCGA-06-6391 TCGA-CS-6665 TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B 
        1.48        51.55        46.88        46.72        31.82        42.05 
TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 TCGA-FG-A60K TCGA-FG-A713 TCGA-FG-A87N 
       62.01        17.16        20.09        17.82        20.45        18.64 
TCGA-HT-A619 TCGA-HW-7490 TCGA-IK-8125 TCGA-R8-A73M TCGA-06-5416 TCGA-06-6701 
       21.40        45.60        42.77        59.38         6.71         4.96 
TCGA-06-A5U0 TCGA-14-1456 TCGA-14-1458 TCGA-14-1821 TCGA-16-1460 TCGA-19-0960 
       26.79        40.96         6.67        17.79         6.41         8.61 
TCGA-27-2521 TCGA-28-1756 TCGA-32-1973 TCGA-32-4208 TCGA-41-4097 TCGA-76-6193 
       16.77         2.83        21.07        21.14         0.20         2.70 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5396 
       43.89        36.36        60.10        40.18         0.26        53.62 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-DB-5270 TCGA-DB-5273 
       37.38        46.95        48.30        49.94       122.73        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5280 
       75.25        47.93        72.92        91.13        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF 
       78.28        18.84        30.21        39.78        37.45        33.57 
TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R 
       72.95        31.63        24.20        30.12         5.98        31.40 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       27.45        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75M TCGA-DB-A75O TCGA-DB-A75P TCGA-DH-5140 TCGA-DH-5142 
       11.24        17.88        30.74        16.18        19.96        63.88 
TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A66G TCGA-DH-A7UR 
       46.06        24.59        27.81        17.19        17.19        54.25 
TCGA-DH-A7US TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       23.21        13.71        18.61        14.56        17.46        13.38 
TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 
        6.81       182.33        18.94        17.49        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       22.42        75.16        46.06        65.75         1.22        87.45 
TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7009 
      114.08         7.96         2.40        62.96       156.23       154.36 
TCGA-DU-7011 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7294 
      105.21       117.40        90.77        30.67        26.30        94.32 
TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7306 
       18.94        44.02        25.91        60.30        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-8168 
        2.76        14.60        21.40        16.96        15.48        14.17 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S2 
       33.27        29.85        31.69        26.17        24.99        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S7 TCGA-DU-A6S8 TCGA-DU-A76R TCGA-DU-A7T6 
       21.57        95.11        20.98        22.29        21.30        17.98 
TCGA-DU-A7T8 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5302 
      139.04        51.52        37.38        44.42        38.89        50.14 
TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 
       67.46        41.13        79.99        57.93       134.27        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK 
       95.57       130.78        29.13        93.21         3.65        12.43 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YW TCGA-E1-A7YY TCGA-E1-A7Z3 
       75.02        15.32         0.76        36.82       146.14        73.48 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 
      145.05        32.35        39.48         0.23         0.20        47.77 
TCGA-FG-5963 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-6691 
       25.48        52.21        36.82        14.93        42.54        41.33 
TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8181 TCGA-FG-8182 
       15.35        17.88        22.55        20.61        28.34        13.68 
TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-8191 TCGA-FG-A4MT 
       14.24        16.01        14.96        22.52        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A6J3 
       18.71        14.76        21.53        15.02        16.44        22.26 
TCGA-FG-A70Y TCGA-FG-A710 TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7467 TCGA-HT-7468 
       28.54        36.66        48.69        27.52         0.10         6.67 
TCGA-HT-7469 TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7475 TCGA-HT-7476 
       11.54        40.11         0.13         0.03        17.42         6.54 
TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7482 TCGA-HT-7483 
        6.38        40.34        75.19        95.93       106.95       172.77 
TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7604 TCGA-HT-7605 
        4.01         5.03        29.85        23.18       122.47         4.57 
TCGA-HT-7606 TCGA-HT-7607 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7610 TCGA-HT-7616 
       17.29         3.16        22.06        45.99        56.09         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7681 TCGA-HT-7684 
       14.27         0.16        16.24         0.76        44.68         6.05 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7693 
        0.10        31.69        14.96         0.10         2.96        17.52 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7856 TCGA-HT-7857 
        6.90        14.53        39.48        19.23        39.09         0.23 
TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7879 
       50.63        23.61        37.15         0.33         0.13         3.68 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 
        5.33        35.47        11.28        31.43         1.64         9.40 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-8107 TCGA-HT-8109 
        0.10        37.87         6.25         0.10         0.46         5.56 
TCGA-HT-8111 TCGA-HT-8113 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-8564 TCGA-HT-A4DV 
        0.23        29.59        34.19        28.27        15.72        26.04 
TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 
        0.13        20.22         0.07         0.10         2.70        16.93 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74K TCGA-HT-A74L 
        1.81        16.83        17.52        10.52        15.35        11.05 
TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 TCGA-HW-7493 
        0.10        56.58        45.44        41.49        68.32        69.27 
TCGA-HW-7495 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-HW-A5KL 
       35.44        40.01        42.54        24.92        31.63        28.87 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EX 
       20.71        19.00        14.40         0.23         6.71         7.99 
TCGA-P5-A5EZ TCGA-P5-A5F0 TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A5F6 
        2.30         9.44         5.88         7.96         7.59         1.28 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A733 
       10.42        13.25        11.64        10.95         9.01        13.61 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A780 
        9.60         7.56        12.23        19.20         3.45         2.37 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CU 
        4.41        15.16        12.62        15.85        14.04        14.83 
TCGA-QH-A6CW TCGA-QH-A6CX TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X3 TCGA-QH-A6X4 
       13.61        12.23        13.41         9.17        10.29        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A86X TCGA-QH-A870 
       16.34        16.73         1.91        16.50        11.08        12.99 
TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 
       88.83        94.03        32.65        30.87         5.46        28.08 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV 
        2.07        19.59        30.67        62.17        87.12        18.77 
TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       41.10        40.93        35.38        36.82        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UA TCGA-S9-A6UB 
       32.61        35.15        98.24        95.93         5.85       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL 
       75.25       135.22        85.55        38.56        84.99        31.10 
TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IS 
       26.47        18.61        18.64        14.07        36.13         7.92 
TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW 
       23.51        20.02         8.19         2.04        20.68        15.06 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 
       28.37        27.16       169.84        99.06        30.05        98.63 
TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C4 TCGA-TM-A7C5 TCGA-TM-A7CA 
       31.59        18.71        20.48        48.33        49.32        34.78 
TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84J TCGA-TM-A84L 
       65.39        59.05        40.64        30.44        24.16        40.83 
TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84R TCGA-TM-A84S TCGA-TM-A84T 
       24.79        33.24        25.38        18.61        14.93        23.80 
TCGA-TQ-A7RF TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK 
       21.37        19.69        15.98         2.04        40.41        44.09 
TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A7RW 
       33.73        31.20        26.14        33.93        61.41        26.99 
TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       31.36        45.93        43.20        13.51         0.10        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-W9-A837 
       20.02        23.47        37.05        16.01        23.21        51.06 
TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C 
       13.32        43.96        39.88        43.40        45.80        46.88 
TCGA-WY-A85D TCGA-WY-A85E TCGA-02-0011 TCGA-02-0014 TCGA-02-0026 TCGA-02-0028 
       37.71        20.81        20.71        82.59        24.59        90.58 
TCGA-02-0047 TCGA-02-0058 TCGA-02-0060 TCGA-02-0069 TCGA-02-0080 TCGA-02-0104 
       14.73         8.35         6.02        28.70        89.72        65.00 
TCGA-02-0107 TCGA-02-0111 TCGA-02-0114 TCGA-02-0338 TCGA-02-0339 TCGA-02-0432 
       17.65        23.18        99.98        10.59        12.39        47.11 
TCGA-06-0129 TCGA-06-0139 TCGA-06-0142 TCGA-06-0160 TCGA-06-0165 TCGA-06-0178 
       33.67        11.90         2.20        11.80        10.65        88.14 
TCGA-06-0240 TCGA-06-0881 TCGA-06-1805 TCGA-06-2569 TCGA-06-2570 TCGA-08-0344 
       20.42        16.57        33.90         0.43        31.50       115.86 
TCGA-08-0350 TCGA-08-0351 TCGA-08-0392 TCGA-08-0516 TCGA-08-0517 TCGA-08-0521 
       29.23        65.33         0.72        19.59        58.68         4.80 
TCGA-08-0524 TCGA-12-0818 TCGA-12-0827 TCGA-15-1444 TCGA-15-1447 TCGA-16-0849 
        7.27        91.76        38.76        50.53        53.19        26.07 
TCGA-16-0850 TCGA-26-1442 
       16.37        31.33 

$subtype3
TCGA-19-A6J4 TCGA-06-5410 TCGA-06-5412 TCGA-06-A7TL TCGA-14-0740 TCGA-14-0781 
        3.98         3.55         4.54        17.72        11.97         0.95 
TCGA-14-3477 TCGA-19-2623 TCGA-19-2625 TCGA-19-5956 TCGA-27-1836 TCGA-27-2527 
        3.78         7.53         4.08        22.49        30.05        14.40 
TCGA-32-1980 TCGA-41-3915 TCGA-76-4934 TCGA-CS-4938 TCGA-CS-6669 TCGA-DB-5277 
        1.18        11.84         2.53       117.50        49.12        50.86 
TCGA-DH-A7UT TCGA-DU-5847 TCGA-DU-7010 TCGA-DU-8163 TCGA-DU-8165 TCGA-E1-A7YV 
       17.46        18.02        14.99        20.68        19.13        32.45 
TCGA-FG-6688 TCGA-FG-7643 TCGA-FG-A4MY TCGA-HT-7473 TCGA-HT-7474 TCGA-HT-7477 
       18.77        20.09        23.70        16.54         3.75        24.26 
TCGA-HT-7611 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7882 TCGA-HT-8013 TCGA-HT-8019 
       57.60        42.74         0.10         3.72        63.55        33.01 
TCGA-HT-8108 TCGA-HT-A74H TCGA-HW-8319 TCGA-HW-A5KK TCGA-P5-A5EY TCGA-QH-A65S 
        2.50         2.43        39.75        12.76         2.37         2.53 
TCGA-QH-A6CS TCGA-RY-A83Z TCGA-S9-A7QX TCGA-TM-A84C TCGA-TM-A84I TCGA-TQ-A7RP 
       19.33         9.90        18.54        16.18        28.08        30.05 
TCGA-TQ-A7RR TCGA-02-0033 TCGA-02-0039 TCGA-02-0052 TCGA-02-0055 TCGA-02-0057 
       25.87         2.83        10.52        12.59         2.50        19.86 
TCGA-02-0084 TCGA-02-0085 TCGA-02-0087 TCGA-02-0113 TCGA-02-0326 TCGA-02-0332 
       12.62        51.32        57.76        92.65         7.33        25.71 
TCGA-02-0456 TCGA-02-2483 TCGA-06-0119 TCGA-06-0127 TCGA-06-0128 TCGA-06-0132 
        3.35        15.32         2.70         3.98        22.72        25.35 
TCGA-06-0141 TCGA-06-0146 TCGA-06-0147 TCGA-06-0159 TCGA-06-0176 TCGA-06-0179 
       10.29        20.09        17.79         9.44        91.00        20.25 
TCGA-06-0189 TCGA-06-0410 TCGA-06-0414 TCGA-06-0650 TCGA-06-6389 TCGA-08-0245 
       15.42         4.70        35.11        23.57         7.79        37.84 
TCGA-08-0512 TCGA-14-0867 TCGA-14-0871 TCGA-19-1385 TCGA-19-1389 TCGA-26-5133 
       42.15         2.04        28.93        10.75         4.64        14.86 
TCGA-26-6174 TCGA-28-2513 TCGA-28-5215 TCGA-28-5216 
        2.33         7.30        11.01        13.64 

subtype1 subtype2 subtype3 
    0.10     0.03     0.10 
subtype1 subtype2 subtype3 
  211.17   182.33   117.50 
subtype1 subtype2 subtype3 
   12.23    23.98    15.37 
[1] "0.1 - 211.2 (12.2)" "0.0 - 182.3 (24.0)" "0.1 - 117.5 (15.4)"
D5V2, continuous
D5V3, binary
          cls
clus         0   1
  subtype1 461  67
  subtype2  57 411
  subtype3  55  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  461   67
  subtype2   57  411
  subtype3   55   34
                        clus
vv                       subtype1 subtype2 subtype3
  BRAIN                       461       57       55
  CENTRAL NERVOUS SYSTEM       67      411       34
[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"
D5V4, binary
          cls
clus         0   1
  subtype1 207 321
  subtype2 200 268
  subtype3  46  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  207  321
  subtype2  200  268
  subtype3   46   43
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      207      200       46
  MALE        321      268       43
[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"
D5V5, binary
          cls
clus         0   1
  subtype1  69 433
  subtype2 170 271
  subtype3  19  66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69  433
  subtype2  170  271
  subtype3   19   66
     clus
vv    subtype1 subtype2 subtype3
  NO        69      170       19
  YES      433      271       66
[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"
D5V6, continuous
          vv
clus       ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA
  subtype1          39                            19               14
  subtype2         137                             6              104
  subtype3          18                             5               11
          vv
clus       OLIGODENDROGLIOMA TREATED PRIMARY GBM
  subtype1                14                  12
  subtype2               170                   4
  subtype3                 5                   2
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             430
  subtype2                              47
  subtype3                              48
D5V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  ASTROCYTOMA                           39      137       18
  GLIOBLASTOMA MULTIFORME (GBM)         19        6        5
  OLIGOASTROCYTOMA                      14      104       11
  OLIGODENDROGLIOMA                     14      170        5
  TREATED PRIMARY GBM                   12        4        2
  UNTREATED PRIMARY (DE NOVO) GBM      430       47       48
[1] 6 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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        45
  subtype2                                0    11                        18
  subtype3                                0     2                         8
          vv
clus       WHITE
  subtype1   452
  subtype2   428
  subtype3    79
D5V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   8       11        2
  BLACK OR AFRICAN AMERICAN              45       18        8
  WHITE                                 452      428       79
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus         0   1
  subtype1   9 443
  subtype2  29 405
  subtype3   6  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  443
  subtype2   29  405
  subtype3    6   73
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            9       29        6
  NOT HISPANIC OR LATINO      443      405       73
[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(6) Variable = METHLYATION_CNMF
D6V1, survival
          sevent
clus2        0   1
  subtype1  58 120
  subtype2 176  48
  subtype3  60  28
  subtype4 136  22
subtype1 subtype2 subtype3 subtype4 
     178      224       88      158 
subtype1 subtype2 subtype3 subtype4 
     120       48       28       22 
$subtype1
TCGA-E1-A7YN TCGA-06-5408 TCGA-06-5411 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 
       23.90        11.74         8.35         8.81         8.98         8.55 
TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6388 
        6.71         2.73         3.75         6.15         4.57         5.23 
TCGA-06-6695 TCGA-06-6699 TCGA-06-6700 TCGA-06-A5U0 TCGA-06-A5U1 TCGA-06-A6S0 
        8.32         1.55         4.77        26.79         1.87         3.12 
TCGA-06-A6S1 TCGA-06-A7TK TCGA-12-5295 TCGA-12-5299 TCGA-12-5301 TCGA-14-0736 
        2.56        14.60        14.93         3.22         2.04        15.12 
TCGA-14-0740 TCGA-14-0862 TCGA-14-1395 TCGA-14-1402 TCGA-14-1450 TCGA-19-4065 
       11.97         2.89         1.38        32.05        58.78         7.04 
TCGA-19-5947 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5953 TCGA-19-5954 
        6.64        17.19         8.02        18.90         4.73        12.10 
TCGA-19-5955 TCGA-19-5956 TCGA-19-5958 TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I 
        1.78        22.49        14.07        16.80        14.96        17.79 
TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 TCGA-26-A7UX TCGA-32-1979 TCGA-32-5222 
        9.40         8.88        18.97        19.33        19.50        19.23 
TCGA-41-5651 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9S TCGA-4W-AA9T TCGA-74-6573 
       15.12        12.46         4.08         1.45        25.58         3.45 
TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6581 TCGA-74-6584 TCGA-76-4925 
       20.91         4.34        14.33         8.22         7.50         4.80 
TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 
        4.54        17.59         3.09         3.65         9.17        47.93 
TCGA-76-4934 TCGA-76-4935 TCGA-76-6191 TCGA-76-6192 TCGA-76-6193 TCGA-76-6282 
        2.53        36.85        16.70         3.29         2.70        17.06 
TCGA-76-6285 TCGA-76-6286 TCGA-76-6656 TCGA-76-6657 TCGA-76-6661 TCGA-76-6662 
        8.35        20.98         4.83         5.03        23.90        34.45 
TCGA-76-6663 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KA TCGA-RR-A6KC TCGA-CS-4941 
       18.64        36.20         5.92         6.28        20.55         7.69 
TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6188 TCGA-DH-5140 TCGA-DU-5847 TCGA-DU-5852 
       21.01        17.69        26.76        19.96        18.02         6.74 
TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6405 TCGA-DU-6406 
        8.45       211.17         7.04        11.64        19.89        16.83 
TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-7292 TCGA-DU-8158 
       11.47         6.54         8.84        10.36         7.96         5.10 
TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TD 
       19.13        24.43        33.96        11.41        26.76         7.50 
TCGA-DU-A7TJ TCGA-E1-A7YD TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7Z2 
        0.56        14.30        19.46        16.18        51.88        13.08 
TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 
       18.44        10.72        18.38        10.78         5.72        11.54 
TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8564 
        0.49         3.72        16.24        12.23        13.78        15.72 
TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A61C TCGA-KT-A7W1 TCGA-P5-A72U 
        0.23        27.35         5.33        17.65        14.40         0.23 
TCGA-QH-A6CV TCGA-QH-A6XC TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7IX 
       14.53        16.70        24.39         5.85        19.86        26.93 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84J TCGA-VW-A8FI TCGA-06-0125 
       54.77        24.92        16.18        24.16         8.05        47.61 
TCGA-06-0152 TCGA-06-0171 TCGA-06-0190 TCGA-06-0210 TCGA-06-0211 TCGA-06-1804 
       12.33        13.12        10.42         7.40        11.84        13.61 
TCGA-06-6693 TCGA-06-6694 TCGA-14-1043 TCGA-19-0957 TCGA-26-5133 TCGA-26-5134 
      120.56         7.36         0.79        21.90        14.86         5.49 
TCGA-26-5139 TCGA-26-6173 TCGA-26-6174 TCGA-28-5204 TCGA-28-5207 TCGA-28-5208 
        1.58         7.92         2.33        14.93        11.28        17.88 
TCGA-28-5209 TCGA-28-5211 TCGA-28-5213 TCGA-28-5214 TCGA-28-5215 TCGA-28-5216 
       14.53        11.77        31.27        23.44        11.01        13.64 
TCGA-28-5218 TCGA-28-5219 TCGA-28-5220 TCGA-28-6450 TCGA-76-6280 TCGA-76-6283 
        5.16        22.68        12.76         5.42        11.38         5.42 
TCGA-76-6660 TCGA-81-5910 TCGA-81-5911 TCGA-87-5896 
        3.75         1.61        17.72        26.30 

$subtype2
TCGA-CS-6665 TCGA-DB-A4XC TCGA-DH-A66B TCGA-DU-A76O TCGA-FG-A87N TCGA-HW-7490 
       51.55        46.72        42.05        17.16        18.64        45.60 
TCGA-06-5417 TCGA-06-6701 TCGA-06-A7TL TCGA-19-A6J5 TCGA-CS-4938 TCGA-CS-4942 
        5.10         4.96        17.72        28.54       117.50        43.89 
TCGA-CS-4943 TCGA-CS-5393 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 
       36.36        40.18        46.95        48.30        81.96        47.93 
TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XD 
       50.86        36.56        78.28        46.42        30.21        39.78 
TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75M 
       37.45        33.57        27.45        18.51        11.24        17.88 
TCGA-DB-A75O TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UT 
       30.74        63.88        46.06        27.81        17.19        17.46 
TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 TCGA-DU-5871 TCGA-DU-5872 
       13.71        18.61        13.38         6.81        18.94        17.49 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-6408 
       49.02        75.16        65.75        87.45        94.52       114.08 
TCGA-DU-6542 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7011 TCGA-DU-7014 
        2.40        62.96       156.23        14.99       105.21       117.40 
TCGA-DU-7015 TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-7306 
       90.77        26.30        44.02        25.91        23.31        41.98 
TCGA-DU-7309 TCGA-DU-8163 TCGA-DU-8166 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
        2.76        20.68        16.96        15.48        33.27        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7T8 TCGA-DU-A7TA 
       31.69        26.17        24.99        20.98       139.04        84.33 
TCGA-DU-A7TC TCGA-DU-A7TI TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5305 
       37.38        38.89        50.14        67.46        41.13        79.99 
TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YU 
      130.78        29.13        93.21         3.65        12.43         0.76 
TCGA-E1-A7YV TCGA-E1-A7YW TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-F6-A8O4 TCGA-FG-5965 
       32.45        36.82       145.05        32.35         0.20        36.82 
TCGA-FG-6689 TCGA-FG-6690 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 
       14.93        42.54        17.88        14.24        14.96        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 
       38.27        18.71        23.70        14.76        21.53        22.26 
TCGA-FG-A70Y TCGA-FG-A711 TCGA-FN-7833 TCGA-HT-7470 TCGA-HT-7472 TCGA-HT-7473 
       28.54        48.69        27.52        40.11         0.03        16.54 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 
       17.42         6.54        24.26       106.95       172.77         4.01 
TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7676 
        5.03       122.47        17.29        45.99        57.60         0.16 
TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7688 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7693 
        6.05        42.74        31.69        14.96         0.10        17.52 
TCGA-HT-7855 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 TCGA-HT-8013 TCGA-HT-8108 
       19.23        23.61         3.68        11.28        63.55         2.50 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 
        0.23        34.19        28.27        20.22         0.10         2.70 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74J TCGA-HT-A74O TCGA-HW-7493 
        1.81        16.83        17.52        10.52         0.10        69.27 
TCGA-HW-8319 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 
       39.75        40.01        42.54        28.87        20.71        19.00 
TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F4 
        0.23         6.71         2.30         5.88         7.96         7.59 
TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A736 
       10.42        13.25         9.01        13.61         9.60         7.56 
TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6X9 TCGA-QH-A6XA 
        2.37         2.53        13.61        10.29         1.91        16.50 
TCGA-QH-A870 TCGA-RY-A83Z TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TU 
       12.99         9.90         2.07        19.59        62.17        87.12 
TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U6 TCGA-S9-A6U8 TCGA-S9-A6U9 
       18.77        36.82        25.81        35.15        98.24        95.93 
TCGA-S9-A6WO TCGA-S9-A7IS TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7QW TCGA-S9-A7QX 
       18.61         7.92        19.99        20.02        15.06        18.54 
TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A7C4 
       99.06        30.05        98.63        31.59        20.48        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84H TCGA-TM-A84I TCGA-TM-A84L TCGA-TM-A84Q 
       34.78        65.39        30.44        28.08        40.83        25.38 
TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       23.80        21.37        15.98        40.41        44.09        36.69 
TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CF 
       25.87        61.41        26.99        31.36        45.93        20.02 
TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A859 TCGA-WY-A85A 
       23.47        16.01        13.32        43.96        39.88        43.40 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-WY-A85E TCGA-06-0221 TCGA-06-6389 
       45.80        46.88        37.71        20.81        19.82         7.79 
TCGA-15-1444 TCGA-26-1442 
       50.53        31.33 

$subtype3
TCGA-06-6391 TCGA-19-A6J4 TCGA-FG-A713 TCGA-06-1806 TCGA-06-5410 TCGA-06-5412 
        1.48         3.98        20.45        15.32         3.55         4.54 
TCGA-06-6697 TCGA-06-6698 TCGA-14-0781 TCGA-32-1980 TCGA-CS-4944 TCGA-CS-5397 
       12.85         4.77         0.95         1.18        60.10         6.38 
TCGA-CS-6290 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-A64O 
       37.38        49.12       122.73        72.92        91.13        25.48 
TCGA-DB-A75P TCGA-DU-5851 TCGA-DU-6404 TCGA-DU-8161 TCGA-DU-8162 TCGA-DU-A7TB 
       16.18        17.46       133.74        23.74        14.60        51.52 
TCGA-DU-A7TG TCGA-E1-A7YM TCGA-E1-A7YY TCGA-E1-A7Z3 TCGA-FG-5963 TCGA-FG-6688 
       44.42        21.30       146.14        73.48        25.48        18.77 
TCGA-FG-6691 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8189 TCGA-HT-7467 
       41.33        20.09        28.34        13.68        22.52         0.10 
TCGA-HT-7474 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7607 
        3.75         6.38        40.34        29.85        23.18         3.16 
TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7680 TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7856 
       56.09        14.27         0.76         0.10        39.48        39.09 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7874 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 
        0.23        50.63        37.15         5.33        35.47        31.43 
TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8106 TCGA-HT-8107 
        1.64         0.10        37.87        33.01         0.10         0.46 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A617 TCGA-HT-A61A 
       29.59        13.74        26.04         0.13        16.14         6.38 
TCGA-HT-A74H TCGA-HW-7489 TCGA-HW-A5KK TCGA-P5-A5EY TCGA-P5-A5F6 TCGA-QH-A6CS 
        2.43        41.49        12.76         2.37         1.28        19.33 
TCGA-QH-A6CX TCGA-S9-A6WG TCGA-S9-A6WI TCGA-S9-A6WN TCGA-S9-A6WQ TCGA-S9-A7IQ 
       12.23        85.55        84.99        26.47        14.07        36.13 
TCGA-S9-A7R2 TCGA-S9-A89V TCGA-TM-A84F TCGA-TM-A84R TCGA-TQ-A7RP TCGA-VM-A8C9 
       10.39        18.71        59.05        18.61        30.05        43.20 
TCGA-VM-A8CD TCGA-06-0650 TCGA-06-6390 TCGA-19-1389 
        7.89        23.57         5.39         4.64 

$subtype4
TCGA-CS-6670 TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K TCGA-HT-A619 
       46.88        31.82        62.01        20.09        17.82        21.40 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5274 
       42.77        59.38         0.26        53.62        49.94        75.25 
TCGA-DB-5279 TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       44.52        18.84        72.95        31.63        24.20        30.12 
TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A75K 
        5.98        31.40        27.81        29.23        14.40        12.10 
TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 
       24.59        30.21        17.19        54.25        23.21        14.56 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 
      182.33        15.16        52.11        22.42        46.06         1.22 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7302 
        7.96       154.36        30.67        94.32        18.94        60.30 
TCGA-DU-8164 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 
       21.40        14.17        25.55        21.57        95.11        22.29 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5318 TCGA-E1-5319 
       21.30        17.98        57.93       134.27        78.21        95.57 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-5962 TCGA-FG-5964 
       75.02        15.32        39.48         0.23        47.77        52.21 
TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-8186 TCGA-FG-A6IZ 
       15.35        40.08        22.55        20.61        16.01        15.02 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7480 TCGA-HT-7481 
       16.44        36.66         6.67         0.13        75.19        95.93 
TCGA-HT-7605 TCGA-HT-7608 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 
        4.57        22.06         0.23        16.24        44.68         0.10 
TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-8012 
        2.96         6.90        14.53         0.33         0.13         9.40 
TCGA-HT-8105 TCGA-HT-8109 TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A74K TCGA-HT-A74L 
        6.25         5.56         0.07        16.93        15.35        11.05 
TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7491 TCGA-HW-7495 TCGA-HW-8322 TCGA-HW-A5KJ 
       56.58        45.44        68.32        35.44        24.92        31.63 
TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5F0 TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A737 
       14.40         7.99         9.44        11.64        10.95        12.23 
TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X 
       19.20         3.45         4.41        15.16        12.62        15.85 
TCGA-QH-A65Z TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 
       14.04        14.83        13.41         9.17        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       16.73        11.08        88.83        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TY 
        5.46        28.08        30.67        41.10        40.93        35.38 
TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH 
       29.85        32.61       123.65        75.25       135.22        38.56 
TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       31.10        18.64        23.51         8.19         2.04        20.68 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M 
       28.37        27.16       169.84        49.32        40.64        24.79 
TCGA-TM-A84O TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO 
       33.24        14.93        19.69         2.04        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VV-A829 
       26.14        33.93        13.51         0.10        39.16        37.05 
TCGA-VW-A7QS TCGA-W9-A837 
       23.21        51.06 

subtype1 subtype2 subtype3 subtype4 
    0.23     0.03     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 
  211.17   172.77   146.14   182.33 
subtype1 subtype2 subtype3 subtype4 
  11.805   26.235   19.050   23.210 
[1] "0.2 - 211.2 (11.8)" "0.0 - 172.8 (26.2)" "0.1 - 146.1 (19.0)"
[4] "0.1 - 182.3 (23.2)"
D6V2, continuous
D6V3, binary
          cls
clus         0   1
  subtype1 118  61
  subtype2   8 217
  subtype3  12  76
  subtype4   0 161
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   61
  subtype2    8  217
  subtype3   12   76
  subtype4    0  161
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  BRAIN                       118        8       12        0
  CENTRAL NERVOUS SYSTEM       61      217       76      161
[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"
D6V4, binary
          cls
clus         0   1
  subtype1  78 101
  subtype2  99 126
  subtype3  40  48
  subtype4  71  90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78  101
  subtype2   99  126
  subtype3   40   48
  subtype4   71   90
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       78       99       40       71
  MALE        101      126       48       90
[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"
D6V5, binary
          cls
clus         0   1
  subtype1  24 138
  subtype2  61 152
  subtype3  31  50
  subtype4  88  64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  138
  subtype2   61  152
  subtype3   31   50
  subtype4   88   64
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        24       61       31       88
  YES      138      152       50       64
[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"
D6V6, continuous
          vv
clus       ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA
  subtype1          38                            16               10
  subtype2         119                             3               66
  subtype3          31                             2               19
  subtype4           6                             0               35
          vv
clus       OLIGODENDROGLIOMA TREATED PRIMARY GBM
  subtype1                13                   1
  subtype2                32                   0
  subtype3                26                   0
  subtype4               120                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             101
  subtype2                               5
  subtype3                              10
  subtype4                               0
D6V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA                           38      119       31        6
  GLIOBLASTOMA MULTIFORME (GBM)         16        3        2        0
  OLIGOASTROCYTOMA                      10       66       19       35
  OLIGODENDROGLIOMA                     13       32       26      120
  TREATED PRIMARY GBM                    1        0        0        0
  UNTREATED PRIMARY (DE NOVO) GBM      101        5       10        0
[1] 6 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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        25
  subtype2                                0     2                         8
  subtype3                                1     1                         7
  subtype4                                0     4                         5
          vv
clus       WHITE
  subtype1   146
  subtype2   214
  subtype3    76
  subtype4   146
D6V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                   1        2        1        4
  BLACK OR AFRICAN AMERICAN              25        8        7        5
  WHITE                                 146      214       76      146
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus         0   1
  subtype1   3 134
  subtype2  14 196
  subtype3   4  75
  subtype4  12 139
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  134
  subtype2   14  196
  subtype3    4   75
  subtype4   12  139
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3       14        4       12
  NOT HISPANIC OR LATINO      134      196       75      139
[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(7) Variable = RPPA_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 127  92
  subtype2 112  56
  subtype3  81  80
  subtype4  65  41
subtype1 subtype2 subtype3 subtype4 
     219      168      161      106 
subtype1 subtype2 subtype3 subtype4 
      92       56       80       41 
$subtype1
TCGA-19-A6J4 TCGA-CS-6670 TCGA-DH-5141 TCGA-DH-A66B TCGA-HW-7490 TCGA-IK-8125 
        3.98        46.88        31.82        42.05        45.60        42.77 
TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5416 TCGA-06-6695 
        3.55         4.54         8.81         8.98         6.71         8.32 
TCGA-06-6697 TCGA-06-A5U1 TCGA-12-3646 TCGA-12-3650 TCGA-16-1460 TCGA-19-1390 
       12.85         1.87        44.02        10.95         6.41        25.38 
TCGA-19-1790 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 TCGA-19-5947 TCGA-19-5952 
        5.06         4.08         7.00         7.04         6.64        18.90 
TCGA-19-5953 TCGA-19-5959 TCGA-26-5132 TCGA-27-1830 TCGA-27-1832 TCGA-27-1833 
        4.73        16.80         9.40         5.06         9.86        24.23 
TCGA-27-1834 TCGA-27-2528 TCGA-28-1750 TCGA-28-1753 TCGA-28-1757 TCGA-32-1978 
       40.54        15.78         8.35         1.22         0.13        15.85 
TCGA-32-1982 TCGA-32-1986 TCGA-32-4211 TCGA-41-3393 TCGA-41-3915 TCGA-41-6646 
        4.67        12.69        12.59         4.44        11.84        12.46 
TCGA-4W-AA9R TCGA-4W-AA9T TCGA-74-6573 TCGA-76-4926 TCGA-76-4927 TCGA-76-4928 
        4.08        25.58         3.45         4.54        17.59         3.09 
TCGA-76-6282 TCGA-76-6656 TCGA-76-6661 TCGA-76-6662 TCGA-RR-A6KA TCGA-CS-4944 
       17.06         4.83        23.90        34.45         6.28        60.10 
TCGA-CS-5393 TCGA-CS-5396 TCGA-CS-6188 TCGA-DB-5275 TCGA-DB-5279 TCGA-DB-5280 
       40.18        53.62        26.76        47.93        44.52        36.56 
TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P 
       78.28        18.84        39.78        31.63        24.20        30.12 
TCGA-DB-A64S TCGA-DB-A75K TCGA-DB-A75L TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A7US 
       27.45        12.10        11.24        24.59        17.19        23.21 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 
       13.38         8.45       182.33        18.94        17.49       211.17 
TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-7011 TCGA-DU-7014 
       46.06        65.75        87.45        94.52       105.21       117.40 
TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7306 TCGA-DU-8167 TCGA-DU-A5TW TCGA-DU-A6S2 
       30.67        26.30        41.98        15.48        24.99        25.55 
TCGA-E1-5303 TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-E1-A7Z6 
       67.46        16.18        51.88        32.45        13.08        32.35 
TCGA-F6-A8O4 TCGA-FG-5964 TCGA-FG-6688 TCGA-FG-7634 TCGA-FG-7637 TCGA-FG-7638 
        0.20        52.21        18.77        15.35        40.08        22.55 
TCGA-FG-7641 TCGA-FG-A4MU TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A70Y TCGA-HT-7471 
       20.61        10.72        18.71        23.70        28.54         0.13 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7483 TCGA-HT-7601 
        0.03        16.54         6.54         6.38       172.77         5.03 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7616 TCGA-HT-7681 TCGA-HT-7684 TCGA-HT-7689 
       22.06        45.99         0.23        44.68         6.05        14.96 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7882 TCGA-HT-8105 TCGA-HT-8106 
       17.52        19.23        50.63         3.72         6.25         0.10 
TCGA-HT-8110 TCGA-HT-A5R9 TCGA-HT-A74O TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-8320 
       13.78         0.07         0.10        45.44        41.49        40.01 
TCGA-HW-8321 TCGA-HW-A5KJ TCGA-P5-A5EV TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 
       42.54        31.63         0.23         5.88         7.96         1.28 
TCGA-P5-A72U TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A736 
        0.23        10.42        13.25        10.95         9.01         7.56 
TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A65X TCGA-QH-A6CW TCGA-QH-A6CX 
       12.23        19.20         2.37        15.85        13.61        12.23 
TCGA-QH-A86X TCGA-QH-A870 TCGA-R8-A6MK TCGA-R8-A6ML TCGA-RY-A83X TCGA-RY-A83Y 
       11.08        12.99        88.83        94.03        30.87         5.46 
TCGA-S9-A6TS TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WE 
       62.17        87.12        18.77        95.93        75.25       135.22 
TCGA-S9-A7IY TCGA-S9-A7IZ TCGA-S9-A7QX TCGA-S9-A7R1 TCGA-S9-A7R4 TCGA-S9-A7R8 
       23.51        19.99        18.54       169.84        30.05        31.59 
TCGA-TM-A7C5 TCGA-TM-A84S TCGA-TQ-A7RF TCGA-TQ-A7RN TCGA-VM-A8C8 TCGA-VM-A8CH 
       49.32        14.93        21.37        33.73        45.93        23.47 
TCGA-VV-A86M TCGA-WY-A85C TCGA-WY-A85D TCGA-02-0003 TCGA-02-0004 TCGA-02-0011 
       16.01        46.88        37.71         4.73        11.34        20.71 
TCGA-02-0068 TCGA-02-0069 TCGA-02-0116 TCGA-02-2470 TCGA-02-2485 TCGA-06-0128 
       26.43        28.70        48.95        12.92        15.45        22.72 
TCGA-06-0130 TCGA-06-0154 TCGA-06-0155 TCGA-06-0171 TCGA-06-0189 TCGA-06-0190 
       12.95        13.94        10.45        13.12        15.42        10.42 
TCGA-06-0238 TCGA-06-0644 TCGA-06-0650 TCGA-06-0882 TCGA-06-1084 TCGA-06-1802 
       13.32        12.62        23.57        20.78        23.93        15.32 
TCGA-06-1805 TCGA-06-2557 TCGA-06-2567 TCGA-06-6389 TCGA-08-0245 TCGA-08-0347 
       33.90         1.08         4.37         7.79        37.84        25.71 
TCGA-08-0348 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 TCGA-08-0358 TCGA-08-0360 
       12.16         1.28         8.42        17.95        22.29        15.39 
TCGA-08-0373 TCGA-08-0375 TCGA-08-0386 TCGA-08-0392 TCGA-15-1447 TCGA-26-5133 
        4.41        12.23        18.02         0.72        53.19        14.86 
TCGA-26-5134 TCGA-28-5214 TCGA-76-6660 
        5.49        23.44         3.75 

$subtype2
TCGA-06-6391 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A713 TCGA-06-5411 TCGA-06-5415 
        1.48        62.01        20.09        20.45         8.35         8.55 
TCGA-06-6388 TCGA-06-6700 TCGA-06-6701 TCGA-06-A6S1 TCGA-12-1597 TCGA-12-3651 
        5.23         4.77         4.96         2.56        22.19        12.69 
TCGA-19-1786 TCGA-19-1788 TCGA-19-1789 TCGA-19-2620 TCGA-19-5958 TCGA-27-1836 
        7.17         3.68         3.25         4.87        14.07        30.05 
TCGA-27-2518 TCGA-28-1747 TCGA-32-1976 TCGA-32-5222 TCGA-41-2573 TCGA-41-5651 
       24.76         2.53         0.49        19.23         8.94        15.12 
TCGA-74-6581 TCGA-76-6192 TCGA-76-6193 TCGA-76-6657 TCGA-76-6663 TCGA-RR-A6KC 
        8.22         3.29         2.70         5.03        18.64        20.55 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4X9 TCGA-DB-A4XB TCGA-DB-A4XE 
       49.12       122.73        91.13        46.42        30.21        37.45 
TCGA-DB-A64O TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75P TCGA-DU-5849 TCGA-DU-5851 
       25.48        27.81        14.40        16.18        14.56        17.46 
TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7302 
      154.36        14.99         7.96        94.32        18.94        60.30 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-A5TP TCGA-DU-A76R 
        2.76        14.60        21.40        16.96        33.27        21.30 
TCGA-DU-A7TB TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YH 
       51.52        44.42        38.89        79.99        57.93        93.21 
TCGA-E1-A7YM TCGA-E1-A7YY TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 
       21.30       146.14        47.77        25.48        36.82        14.93 
TCGA-FG-6690 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A6IZ TCGA-FG-A70Z 
       42.54        20.09        28.34        22.52        15.02        10.78 
TCGA-FG-A87Q TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7480 
        5.72         0.10        40.11         3.75        17.42        75.19 
TCGA-HT-7481 TCGA-HT-7485 TCGA-HT-7602 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 
       95.93         4.01        29.85        23.18         4.57         3.16 
TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 
       56.09        14.27         0.10        31.69         6.90        14.53 
TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       39.09        37.15         0.13         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8107 
       31.43         1.64         0.10        37.87        33.01         0.46 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 
        5.56        29.59        13.74        15.72        26.04        20.22 
TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61A TCGA-HT-A74L 
        0.10         2.70         1.81        16.14         6.38        11.05 
TCGA-HW-7486 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8322 TCGA-KT-A74X TCGA-P5-A5EX 
       56.58        69.27        35.44        24.92        14.40         7.99 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A733 TCGA-P5-A735 TCGA-P5-A77X 
        9.44         7.59        11.64        13.61         9.60         3.45 
TCGA-P5-A781 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A6CS TCGA-QH-A6CY TCGA-QH-A6CZ 
        4.41         2.53        12.62        19.33        13.41         9.17 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50        16.70 
TCGA-R8-A6MO TCGA-RY-A843 TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WG TCGA-S9-A6WP 
       32.65         2.07        35.38        35.15        85.55        18.64 
TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7QZ TCGA-TM-A84R TCGA-TQ-A7RR 
       14.07        36.13         8.19        27.16        18.61        25.87 
TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-02-0014 TCGA-06-1804 TCGA-06-2558 TCGA-06-2564 
       26.99         7.89        82.59        13.61        12.49         5.95 
TCGA-06-2566 TCGA-06-2570 TCGA-08-0344 TCGA-08-0359 TCGA-14-0813 TCGA-15-1449 
        5.98        31.50       115.86         3.39         1.35        13.28 
TCGA-16-0846 TCGA-19-0957 TCGA-19-0962 TCGA-19-1389 TCGA-26-1442 TCGA-26-6174 
        3.91        21.90         0.66         4.64        31.33         2.33 

$subtype3
TCGA-DB-A4XC TCGA-DU-A76O TCGA-FG-A87N TCGA-HT-A619 TCGA-06-5408 TCGA-06-5417 
       46.72        17.16        18.64        21.40        11.74         5.10 
TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-06-6698 TCGA-06-6699 TCGA-06-A5U0 
        3.75         6.15         4.57         4.77         1.55        26.79 
TCGA-06-A6S0 TCGA-06-A7TL TCGA-12-1598 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
        3.12        17.72        15.65        34.92        14.53        14.93 
TCGA-12-5301 TCGA-19-1392 TCGA-19-1791 TCGA-19-2619 TCGA-19-4068 TCGA-19-5951 
        2.04         3.65         0.13         9.67         4.50         8.02 
TCGA-19-5954 TCGA-19-5956 TCGA-19-5960 TCGA-19-A60I TCGA-19-A6J5 TCGA-26-A7UX 
       12.10        22.49        14.96        17.79        28.54        19.33 
TCGA-27-1831 TCGA-28-1746 TCGA-28-1760 TCGA-32-1970 TCGA-32-1987 TCGA-32-1991 
       16.60         0.20         4.70        15.39        14.86        16.93 
TCGA-32-4210 TCGA-41-2575 TCGA-74-6577 TCGA-74-6578 TCGA-74-6584 TCGA-76-4929 
        3.72         9.53         4.34        14.33         7.50         3.65 
TCGA-76-4931 TCGA-76-4932 TCGA-76-6285 TCGA-76-6664 TCGA-OX-A56R TCGA-CS-4943 
        9.17        47.93         8.35        36.20         5.92        36.36 
TCGA-CS-5394 TCGA-CS-5397 TCGA-CS-6666 TCGA-CS-6668 TCGA-DB-5274 TCGA-DB-5277 
        0.26         6.38        46.95        49.94        75.25        50.86 
TCGA-DB-A4XG TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64X TCGA-DH-5140 TCGA-DH-5142 
       72.95         5.98        31.40        18.51        19.96        63.88 
TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5855 TCGA-DU-6393 TCGA-DU-6394 
       17.19        18.02         6.74         6.81        52.11        22.42 
TCGA-DU-6396 TCGA-DU-6400 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
       75.16         1.22         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 
       16.83       114.08         7.96         2.40        11.47        62.96 
TCGA-DU-7008 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8165 TCGA-DU-8168 TCGA-DU-A5TT 
      156.23         8.84        10.36        19.13        14.17        24.43 
TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76L 
       26.17        33.96        21.57        22.29        11.41        26.76 
TCGA-DU-A7T6 TCGA-DU-A7TA TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5304 TCGA-E1-5311 
       17.98        84.33         7.50         0.56        41.13       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YI TCGA-E1-A7YS TCGA-E1-A7Z3 TCGA-EZ-7264 
       78.21        95.57         3.65        15.32        73.48        39.48 
TCGA-F6-A8O3 TCGA-FG-6691 TCGA-FG-7636 TCGA-FG-A4MT TCGA-FG-A6J3 TCGA-FG-A710 
        0.23        41.33        17.88        38.27        22.26        36.66 
TCGA-HT-7469 TCGA-HT-7477 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7677 TCGA-HT-7690 
       11.54        24.26       122.47        17.29        16.24         0.10 
TCGA-HT-7857 TCGA-HT-7875 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-A615 TCGA-HT-A61B 
        0.23         0.33        16.24         9.40        16.93        17.52 
TCGA-HW-7491 TCGA-HW-A5KK TCGA-HW-A5KM TCGA-QH-A6CV TCGA-RY-A83Z TCGA-S9-A6U1 
       68.32        12.76        20.71        14.53         9.90        25.81 
TCGA-S9-A6WH TCGA-S9-A7IS TCGA-S9-A7J0 TCGA-S9-A7J2 TCGA-TQ-A7RQ TCGA-TQ-A8XE 
       38.56         7.92        20.02         2.04        26.14        31.36 
TCGA-VM-A8CB TCGA-VV-A829 TCGA-VW-A7QS TCGA-06-0125 TCGA-06-0126 TCGA-06-0129 
        0.10        37.05        23.21        47.61         6.94        33.67 
TCGA-06-0156 TCGA-06-0875 TCGA-06-0876 TCGA-06-0878 TCGA-06-0879 TCGA-06-1086 
        5.85        43.46        46.19         7.17        40.41         6.84 
TCGA-06-1087 TCGA-06-1800 TCGA-06-2559 TCGA-06-2563 TCGA-06-2565 TCGA-06-6693 
        4.04        26.79         4.93        30.64        16.64       120.56 
TCGA-06-6694 TCGA-08-0350 TCGA-08-0356 TCGA-08-0389 TCGA-12-0692 TCGA-14-0871 
        7.36        29.23        31.10        15.35         3.65        28.93 
TCGA-19-1386 TCGA-26-6173 TCGA-28-5208 TCGA-76-6283 TCGA-81-5910 
        9.07         7.92        17.88         5.42         1.61 

$subtype4
TCGA-CS-6665 TCGA-E1-A7YN TCGA-06-1806 TCGA-06-5418 TCGA-12-1599 TCGA-12-3649 
       51.55        23.90        15.32         2.73        25.68        15.22 
TCGA-14-0862 TCGA-14-1823 TCGA-19-5950 TCGA-19-5955 TCGA-26-1440 TCGA-28-1752 
        2.89        17.85        17.19         1.78         9.73         8.48 
TCGA-41-3392 TCGA-41-4097 TCGA-4W-AA9S TCGA-74-6575 TCGA-CS-4938 TCGA-CS-4942 
        0.99         0.20         1.45        20.91       117.50        43.89 
TCGA-CS-6186 TCGA-DB-5273 TCGA-DB-5276 TCGA-DB-A4XF TCGA-DB-A64V TCGA-DB-A75M 
       17.69        81.96        72.92        33.57        29.23        17.88 
TCGA-DB-A75O TCGA-DH-5143 TCGA-DH-A66D TCGA-DU-5874 TCGA-DU-6395 TCGA-DU-7012 
       30.74        46.06        27.81        15.16        49.02         6.54 
TCGA-DU-7015 TCGA-DU-7301 TCGA-DU-7304 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8163 
       90.77        25.91        23.31         5.10        23.74        20.68 
TCGA-DU-A5TR TCGA-DU-A5TS TCGA-E1-5302 TCGA-E1-5322 TCGA-E1-A7YJ TCGA-E1-A7YW 
       29.85        31.69        50.14       130.78        19.46        36.82 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MW 
       13.68        14.24        16.01        14.96        32.61        18.38 
TCGA-FG-A60J TCGA-FG-A60L TCGA-HT-7468 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7611 
       14.76        21.53         6.67        40.34       106.95        57.60 
TCGA-HT-7676 TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7854 
        0.16         0.76        42.74         0.10         2.96        39.48 
TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8111 
        0.49        23.61         3.68        63.55        12.23         0.23 
TCGA-HT-8114 TCGA-HT-A5R5 TCGA-HT-A618 TCGA-HT-A74H TCGA-HT-A74J TCGA-HW-8319 
       34.19         0.13        16.83         2.43        10.52        39.75 
TCGA-IK-7675 TCGA-P5-A5EW TCGA-P5-A5EY TCGA-P5-A5EZ TCGA-QH-A65Z TCGA-QH-A6CU 
       19.00         6.71         2.37         2.30        14.04        14.83 
TCGA-RY-A845 TCGA-S9-A6TX TCGA-S9-A6U0 TCGA-S9-A6U5 TCGA-S9-A6WN TCGA-TQ-A7RG 
       19.59        40.93        24.39        32.61        26.47        19.69 
TCGA-TQ-A7RH TCGA-TQ-A7RK TCGA-TQ-A7RV TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE 
       15.98        44.09        61.41        43.20        13.51        39.16 
TCGA-W9-A837 TCGA-WY-A85B TCGA-06-0939 TCGA-06-2562 TCGA-06-6390 TCGA-08-0345 
       51.06        45.80        26.76        12.56         5.39         1.74 
TCGA-08-0346 TCGA-08-0349 TCGA-08-0351 TCGA-08-0355 TCGA-08-0357 TCGA-08-0380 
        8.42         9.80        65.33        24.56        37.58        14.93 
TCGA-08-0385 TCGA-08-0390 TCGA-12-0691 TCGA-15-1446 
        2.70        13.97        12.13        19.10 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  211.17   154.36   156.23   130.78 
subtype1 subtype2 subtype3 subtype4 
   17.06    15.93    16.83    19.05 
[1] "0.0 - 211.2 (17.1)" "0.1 - 154.4 (15.9)" "0.1 - 156.2 (16.8)"
[4] "0.1 - 130.8 (19.1)"
D7V2, continuous
D7V3, binary
          cls
clus         0   1
  subtype1  90 129
  subtype2  44 127
  subtype3  69  92
  subtype4  29  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90  129
  subtype2   44  127
  subtype3   69   92
  subtype4   29   80
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  BRAIN                        90       44       69       29
  CENTRAL NERVOUS SYSTEM      129      127       92       80
[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"
D7V4, binary
          cls
clus         0   1
  subtype1  77 142
  subtype2  80  91
  subtype3  85  76
  subtype4  41  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77  142
  subtype2   80   91
  subtype3   85   76
  subtype4   41   68
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       77       80       85       41
  MALE        142       91       76       68
[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"
D7V5, binary
          cls
clus         0   1
  subtype1  52 150
  subtype2  57 106
  subtype3  38 112
  subtype4  34  63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52  150
  subtype2   57  106
  subtype3   38  112
  subtype4   34   63
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        52       57       38       34
  YES      150      106      112       63
[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"
D7V6, continuous
          vv
clus       ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA
  subtype1          44                             6               37
  subtype2          32                             3               35
  subtype3          36                             8               15
  subtype4          35                             2               27
          vv
clus       OLIGODENDROGLIOMA TREATED PRIMARY GBM
  subtype1                48                   2
  subtype2                60                   0
  subtype3                41                   1
  subtype4                18                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              82
  subtype2                              41
  subtype3                              60
  subtype4                              27
D7V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA                           44       32       36       35
  GLIOBLASTOMA MULTIFORME (GBM)          6        3        8        2
  OLIGOASTROCYTOMA                      37       35       15       27
  OLIGODENDROGLIOMA                     48       60       41       18
  TREATED PRIMARY GBM                    2        0        1        0
  UNTREATED PRIMARY (DE NOVO) GBM       82       41       60       27
[1] 6 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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                        18
  subtype2                                1     3                         8
  subtype3                                0     7                        14
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1   193
  subtype2   156
  subtype3   133
  subtype4    96
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   2        3        7        0
  BLACK OR AFRICAN AMERICAN              18        8       14        5
  WHITE                                 193      156      133       96
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus         0   1
  subtype1  11 190
  subtype2   7 154
  subtype3   3 140
  subtype4   8  89
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11  190
  subtype2    7  154
  subtype3    3  140
  subtype4    8   89
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           11        7        3        8
  NOT HISPANIC OR LATINO      190      154      140       89
[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(8) Variable = RPPA_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 120 120
  subtype2 157  98
  subtype3 108  51
subtype1 subtype2 subtype3 
     240      255      159 
subtype1 subtype2 subtype3 
     120       98       51 
$subtype1
TCGA-19-A6J4 TCGA-CS-6665 TCGA-DH-A66B TCGA-E1-A7YN TCGA-FG-A87N TCGA-HT-A619 
        3.98        51.55        42.05        23.90        18.64        21.40 
TCGA-HW-7490 TCGA-06-5410 TCGA-06-5412 TCGA-06-5416 TCGA-06-5418 TCGA-06-5858 
       45.60         3.55         4.54         6.71         2.73         6.15 
TCGA-06-6695 TCGA-06-6697 TCGA-06-6698 TCGA-06-A5U1 TCGA-12-1598 TCGA-12-5301 
        8.32        12.85         4.77         1.87        15.65         2.04 
TCGA-14-0862 TCGA-19-1392 TCGA-19-1790 TCGA-19-2625 TCGA-19-2631 TCGA-19-4065 
        2.89         3.65         5.06         4.08         7.00         7.04 
TCGA-19-5947 TCGA-19-5953 TCGA-19-5954 TCGA-19-5955 TCGA-19-A6J5 TCGA-27-1830 
        6.64         4.73        12.10         1.78        28.54         5.06 
TCGA-27-1832 TCGA-28-1750 TCGA-28-1753 TCGA-28-1760 TCGA-32-1986 TCGA-32-1987 
        9.86         8.35         1.22         4.70        12.69        14.86 
TCGA-32-4211 TCGA-41-3915 TCGA-41-4097 TCGA-41-6646 TCGA-4W-AA9R TCGA-4W-AA9T 
       12.59        11.84         0.20        12.46         4.08        25.58 
TCGA-74-6573 TCGA-74-6575 TCGA-74-6577 TCGA-74-6578 TCGA-76-4926 TCGA-76-4928 
        3.45        20.91         4.34        14.33         4.54         3.09 
TCGA-76-4929 TCGA-76-6661 TCGA-76-6662 TCGA-RR-A6KA TCGA-CS-4943 TCGA-CS-5393 
        3.65        23.90        34.45         6.28        36.36        40.18 
TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6666 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-5281 
       53.62         6.38        46.95        50.86        36.56        78.28 
TCGA-DB-A4XA TCGA-DB-A4XG TCGA-DB-A64P TCGA-DB-A64R TCGA-DB-A64S TCGA-DB-A75K 
       18.84        72.95        30.12        31.40        27.45        12.10 
TCGA-DB-A75L TCGA-DH-5140 TCGA-DH-A66G TCGA-DU-5847 TCGA-DU-5855 TCGA-DU-5871 
       11.24        19.96        17.19        18.02         6.81        18.94 
TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6396 TCGA-DU-6397 
       17.49       211.17        52.11        22.42        75.16        46.06 
TCGA-DU-6400 TCGA-DU-6401 TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        1.22        87.45         7.04       133.74        19.89        16.83 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7008 TCGA-DU-7011 
        7.96         2.40        11.47        62.96       156.23       105.21 
TCGA-DU-7012 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7019 TCGA-DU-7290 
        6.54       117.40        90.77        30.67        26.30        10.36 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT 
       25.91        41.98         5.10        23.74        19.13        24.43 
TCGA-DU-A5TW TCGA-DU-A6S2 TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7T6 TCGA-DU-A7TA 
       24.99        25.55        11.41        26.76        17.98        84.33 
TCGA-E1-5303 TCGA-E1-5318 TCGA-E1-5322 TCGA-E1-A7YI TCGA-E1-A7YL TCGA-E1-A7YQ 
       67.46        78.21       130.78         3.65        16.18        51.88 
TCGA-E1-A7YS TCGA-E1-A7YV TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-5964 
       15.32        32.45        13.08        73.48         0.20        52.21 
TCGA-FG-7637 TCGA-FG-8185 TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A70Y TCGA-HT-7469 
       40.08        14.24        18.71        23.70        28.54        11.54 
TCGA-HT-7471 TCGA-HT-7473 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7480 
        0.13        16.54         6.54        24.26         6.38        75.19 
TCGA-HT-7483 TCGA-HT-7601 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7616 
      172.77         5.03       122.47        17.29        45.99         0.23 
TCGA-HT-7684 TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7874 
        6.05        17.52        19.23         0.23         0.49        37.15 
TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8012 TCGA-HT-8105 TCGA-HT-8106 TCGA-HT-A5R9 
        3.72        16.24         9.40         6.25         0.10         0.07 
TCGA-HT-A74O TCGA-HW-7489 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-A5KJ TCGA-HW-A5KM 
        0.10        41.49        40.01        42.54        31.63        20.71 
TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-P5-A72W 
       19.00         0.23         7.96         1.28         0.23        10.42 
TCGA-P5-A730 TCGA-P5-A780 TCGA-QH-A65X TCGA-QH-A6CX TCGA-QH-A6X5 TCGA-QH-A86X 
       10.95         2.37        15.85        12.23        16.34        11.08 
TCGA-QH-A870 TCGA-RY-A83X TCGA-RY-A83Y TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6U0 
       12.99        30.87         5.46        87.12        18.77        24.39 
TCGA-S9-A6U1 TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WH TCGA-S9-A6WN TCGA-S9-A7IS 
       25.81        95.93        75.25        38.56        26.47         7.92 
TCGA-S9-A7IZ TCGA-S9-A7J0 TCGA-S9-A7J2 TCGA-S9-A7QX TCGA-S9-A7R1 TCGA-S9-A7R4 
       19.99        20.02         2.04        18.54       169.84        30.05 
TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TQ-A7RF TCGA-TQ-A7RQ TCGA-VM-A8C8 TCGA-VM-A8CB 
       31.59        49.32        21.37        26.14        45.93         0.10 
TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WY-A85C TCGA-02-0003 TCGA-02-0004 
       37.05        16.01        23.21        46.88         4.73        11.34 
TCGA-02-0068 TCGA-02-0116 TCGA-02-2470 TCGA-06-0125 TCGA-06-0128 TCGA-06-0130 
       26.43        48.95        12.92        47.61        22.72        12.95 
TCGA-06-0156 TCGA-06-0171 TCGA-06-0189 TCGA-06-0190 TCGA-06-0238 TCGA-06-0644 
        5.85        13.12        15.42        10.42        13.32        12.62 
TCGA-06-0875 TCGA-06-0879 TCGA-06-0882 TCGA-06-1084 TCGA-06-1086 TCGA-06-1087 
       43.46        40.41        20.78        23.93         6.84         4.04 
TCGA-06-1800 TCGA-06-1802 TCGA-06-2559 TCGA-06-2562 TCGA-06-6694 TCGA-08-0245 
       26.79        15.32         4.93        12.56         7.36        37.84 
TCGA-08-0345 TCGA-08-0346 TCGA-08-0348 TCGA-08-0350 TCGA-08-0356 TCGA-08-0360 
        1.74         8.42        12.16        29.23        31.10        15.39 
TCGA-08-0385 TCGA-08-0390 TCGA-08-0392 TCGA-12-0692 TCGA-14-0871 TCGA-15-1447 
        2.70        13.97         0.72         3.65        28.93        53.19 
TCGA-26-5133 TCGA-26-5134 TCGA-28-5208 TCGA-76-6283 TCGA-76-6660 TCGA-81-5910 
       14.86         5.49        17.88         5.42         3.75         1.61 

$subtype2
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-A76O TCGA-IK-8125 TCGA-06-1806 TCGA-06-5408 
       46.72        31.82        17.16        42.77        15.32        11.74 
TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5417 TCGA-06-5856 TCGA-06-5859 
        8.81         8.98         8.55         5.10         3.75         4.57 
TCGA-06-6699 TCGA-06-6701 TCGA-06-A5U0 TCGA-06-A6S0 TCGA-06-A6S1 TCGA-06-A7TL 
        1.55         4.96        26.79         3.12         2.56        17.72 
TCGA-12-1599 TCGA-12-3646 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 
       25.68        44.02        10.95        34.92        14.53        14.93 
TCGA-14-1823 TCGA-16-1460 TCGA-19-1786 TCGA-19-1789 TCGA-19-1791 TCGA-19-2619 
       17.85         6.41         7.17         3.25         0.13         9.67 
TCGA-19-4068 TCGA-19-5950 TCGA-19-5951 TCGA-19-5952 TCGA-19-5956 TCGA-19-5958 
        4.50        17.19         8.02        18.90        22.49        14.07 
TCGA-19-5959 TCGA-19-5960 TCGA-19-A60I TCGA-26-1440 TCGA-26-5132 TCGA-26-A7UX 
       16.80        14.96        17.79         9.73         9.40        19.33 
TCGA-27-1831 TCGA-27-1833 TCGA-27-1834 TCGA-27-2528 TCGA-28-1746 TCGA-28-1747 
       16.60        24.23        40.54        15.78         0.20         2.53 
TCGA-28-1752 TCGA-28-1757 TCGA-32-1970 TCGA-32-1978 TCGA-32-1982 TCGA-32-1991 
        8.48         0.13        15.39        15.85         4.67        16.93 
TCGA-32-4210 TCGA-32-5222 TCGA-41-2575 TCGA-41-3392 TCGA-41-3393 TCGA-41-5651 
        3.72        19.23         9.53         0.99         4.44        15.12 
TCGA-4W-AA9S TCGA-74-6584 TCGA-76-4931 TCGA-76-4932 TCGA-76-6282 TCGA-76-6285 
        1.45         7.50         9.17        47.93        17.06         8.35 
TCGA-76-6656 TCGA-76-6657 TCGA-76-6664 TCGA-OX-A56R TCGA-RR-A6KC TCGA-CS-4938 
        4.83         5.03        36.20         5.92        20.55       117.50 
TCGA-CS-4942 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6668 
       43.89        60.10         0.26        17.69        26.76        49.94 
TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5279 TCGA-DB-A4X9 
       81.96        75.25        47.93        72.92        44.52        46.42 
TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64L TCGA-DB-A64Q TCGA-DB-A64V 
       39.78        37.45        33.57        24.20         5.98        29.23 
TCGA-DB-A64X TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5142 TCGA-DH-5143 TCGA-DH-5144 
       18.51        17.88        30.74        63.88        46.06        24.59 
TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7US TCGA-DU-5852 TCGA-DU-5853 TCGA-DU-5854 
       27.81        17.19        23.21         6.74        13.38         8.45 
TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6399 TCGA-DU-6403 TCGA-DU-6407 TCGA-DU-6408 
      182.33        15.16        65.75        11.64        94.52       114.08 
TCGA-DU-7013 TCGA-DU-7292 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-8163 TCGA-DU-8164 
        8.84         7.96        60.30        23.31        20.68        21.40 
TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A5TY 
       15.48        14.17        33.27        29.85        26.17        33.96 
TCGA-DU-A6S3 TCGA-DU-A6S8 TCGA-DU-A7TD TCGA-DU-A7TI TCGA-DU-A7TJ TCGA-E1-5302 
       21.57        22.29         7.50        38.89         0.56        50.14 
TCGA-E1-5304 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-5319 TCGA-E1-A7YJ TCGA-E1-A7YW 
       41.13        57.93       134.27        95.57        19.46        36.82 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-6688 TCGA-FG-6690 TCGA-FG-6691 
       32.35        39.48         0.23        18.77        42.54        41.33 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MU TCGA-FG-A4MW 
       17.88        22.55        32.61        38.27        10.72        18.38 
TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A6J3 TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7472 
       21.53        15.02        22.26        36.66         6.67         0.03 
TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7608 TCGA-HT-7611 TCGA-HT-7676 
       40.34       106.95         4.01        22.06        57.60         0.16 
TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7687 TCGA-HT-7689 TCGA-HT-7690 
       16.24         0.76        42.74         0.10        14.96         0.10 
TCGA-HT-7691 TCGA-HT-7692 TCGA-HT-7854 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7875 
        0.10         2.96        39.48        50.63        23.61         0.33 
TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8114 
        3.68        63.55        12.23        13.78         0.23        34.19 
TCGA-HT-A5R5 TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74H TCGA-HW-7491 
        0.13        16.93        16.83        17.52         2.43        68.32 
TCGA-HW-A5KK TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72X TCGA-P5-A731 
       12.76         6.71         2.30         5.88        13.25         9.01 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-QH-A65S TCGA-QH-A6CV TCGA-QH-A6CW 
        9.60         7.56        12.23         2.53        14.53        13.61 
TCGA-QH-A6CZ TCGA-QH-A6XC TCGA-R8-A6MK TCGA-R8-A6ML TCGA-RY-A83Z TCGA-RY-A845 
        9.17        16.70        88.83        94.03         9.90        19.59 
TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6WE TCGA-S9-A6WG 
       62.17        35.38        32.61        35.15       135.22        85.55 
TCGA-S9-A7IY TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RK TCGA-TQ-A7RN 
       23.51        14.93        19.69        15.98        44.09        33.73 
TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8C9 TCGA-VM-A8CA TCGA-VM-A8CE TCGA-VM-A8CH 
       61.41        31.36        43.20        13.51        39.16        23.47 
TCGA-W9-A837 TCGA-WY-A85B TCGA-WY-A85D TCGA-02-0011 TCGA-02-2485 TCGA-06-0126 
       51.06        45.80        37.71        20.71        15.45         6.94 
TCGA-06-0129 TCGA-06-0154 TCGA-06-0155 TCGA-06-0876 TCGA-06-0878 TCGA-06-0939 
       33.67        13.94        10.45        46.19         7.17        26.76 
TCGA-06-2557 TCGA-06-2563 TCGA-06-2565 TCGA-06-2567 TCGA-06-6389 TCGA-06-6390 
        1.08        30.64        16.64         4.37         7.79         5.39 
TCGA-06-6693 TCGA-08-0344 TCGA-08-0349 TCGA-08-0352 TCGA-08-0353 TCGA-08-0354 
      120.56       115.86         9.80         1.28         8.42        17.95 
TCGA-08-0355 TCGA-08-0357 TCGA-08-0358 TCGA-08-0375 TCGA-08-0380 TCGA-08-0386 
       24.56        37.58        22.29        12.23        14.93        18.02 
TCGA-08-0389 TCGA-12-0691 TCGA-14-0813 TCGA-15-1446 TCGA-19-0962 TCGA-19-1386 
       15.35        12.13         1.35        19.10         0.66         9.07 
TCGA-26-1442 TCGA-26-6173 TCGA-28-5214 
       31.33         7.92        23.44 

$subtype3
TCGA-06-6391 TCGA-CS-6670 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A713 TCGA-06-5411 
        1.48        46.88        62.01        20.09        20.45         8.35 
TCGA-06-6388 TCGA-06-6700 TCGA-12-1597 TCGA-12-3649 TCGA-12-3651 TCGA-19-1390 
        5.23         4.77        22.19        15.22        12.69        25.38 
TCGA-19-1788 TCGA-19-2620 TCGA-27-1836 TCGA-27-2518 TCGA-32-1976 TCGA-41-2573 
        3.68         4.87        30.05        24.76         0.49         8.94 
TCGA-74-6581 TCGA-76-4927 TCGA-76-6192 TCGA-76-6193 TCGA-76-6663 TCGA-CS-6669 
        8.22        17.59         3.29         2.70        18.64        49.12 
TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4XB TCGA-DB-A4XH TCGA-DB-A64O TCGA-DB-A64U 
      122.73        91.13        30.21        31.63        25.48        27.81 
TCGA-DB-A64W TCGA-DB-A75P TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6395 TCGA-DU-7009 
       14.40        16.18        14.56        17.46        49.02       154.36 
TCGA-DU-7010 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8166 
       14.99        94.32        18.94         2.76        14.60        16.96 
TCGA-DU-A5TS TCGA-DU-A76R TCGA-DU-A7TB TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-A7YH 
       31.69        21.30        51.52        44.42        79.99        93.21 
TCGA-E1-A7YM TCGA-E1-A7YY TCGA-FG-5962 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6689 
       21.30       146.14        47.77        25.48        36.82        14.93 
TCGA-FG-7634 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8182 TCGA-FG-8186 
       15.35        20.61        20.09        28.34        13.68        16.01 
TCGA-FG-8188 TCGA-FG-8189 TCGA-FG-A60J TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7467 
       14.96        22.52        14.76        10.78         5.72         0.10 
TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7481 TCGA-HT-7602 TCGA-HT-7603 
       40.11         3.75        17.42        95.93        29.85        23.18 
TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7681 TCGA-HT-7688 
        4.57         3.16        56.09        14.27        44.68        31.69 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 
        6.90        14.53        39.09         0.13         5.33        35.47 
TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       11.28        31.43         1.64         0.10        37.87        33.01 
TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV 
        0.46         5.56        29.59        13.74        15.72        26.04 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A616 TCGA-HT-A617 TCGA-HT-A61A 
       20.22         0.10         2.70         1.81        16.14         6.38 
TCGA-HT-A74J TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7493 TCGA-HW-7495 
       10.52        11.05        56.58        45.44        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8322 TCGA-KT-A74X TCGA-P5-A5EX TCGA-P5-A5EY TCGA-P5-A5F0 
       39.75        24.92        14.40         7.99         2.37         9.44 
TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A733 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 
        7.59        11.64        13.61        19.20         3.45         4.41 
TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CY TCGA-QH-A6X4 
       12.62        14.04        19.33        14.83        13.41        14.53 
TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-R8-A6MO TCGA-RY-A843 TCGA-S9-A6TX 
       16.73         1.91        16.50        32.65         2.07        40.93 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7J1 TCGA-S9-A7QZ TCGA-TM-A84R 
       18.64        14.07        36.13         8.19        27.16        18.61 
TCGA-TQ-A7RR TCGA-TQ-A7RW TCGA-VM-A8CD TCGA-02-0014 TCGA-02-0069 TCGA-06-0650 
       25.87        26.99         7.89        82.59        28.70        23.57 
TCGA-06-1804 TCGA-06-1805 TCGA-06-2558 TCGA-06-2564 TCGA-06-2566 TCGA-06-2570 
       13.61        33.90        12.49         5.95         5.98        31.50 
TCGA-08-0347 TCGA-08-0351 TCGA-08-0359 TCGA-08-0373 TCGA-15-1449 TCGA-16-0846 
       25.71        65.33         3.39         4.41        13.28         3.91 
TCGA-19-0957 TCGA-19-1389 TCGA-26-6174 
       21.90         4.64         2.33 

subtype1 subtype2 subtype3 
    0.07     0.03     0.10 
subtype1 subtype2 subtype3 
  211.17   182.33   154.36 
subtype1 subtype2 subtype3 
   16.21    17.19    16.50 
[1] "0.1 - 211.2 (16.2)" "0.0 - 182.3 (17.2)" "0.1 - 154.4 (16.5)"
D8V2, continuous
D8V3, binary
          cls
clus         0   1
  subtype1  90 151
  subtype2 104 152
  subtype3  38 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   90  151
  subtype2  104  152
  subtype3   38  125
                        clus
vv                       subtype1 subtype2 subtype3
  BRAIN                        90      104       38
  CENTRAL NERVOUS SYSTEM      151      152      125
[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"
D8V4, binary
          cls
clus         0   1
  subtype1 105 136
  subtype2 100 156
  subtype3  78  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105  136
  subtype2  100  156
  subtype3   78   85
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      105      100       78
  MALE        136      156       85
[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"
D8V5, binary
          cls
clus         0   1
  subtype1  56 166
  subtype2  66 173
  subtype3  59  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56  166
  subtype2   66  173
  subtype3   59   92
     clus
vv    subtype1 subtype2 subtype3
  NO        56       66       59
  YES      166      173       92
[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"
D8V6, continuous
          vv
clus       ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA
  subtype1          61                             8               33
  subtype2          61                            10               43
  subtype3          25                             1               38
          vv
clus       OLIGODENDROGLIOMA TREATED PRIMARY GBM
  subtype1                57                   2
  subtype2                48                   1
  subtype3                62                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                              80
  subtype2                              93
  subtype3                              37
D8V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  ASTROCYTOMA                           61       61       25
  GLIOBLASTOMA MULTIFORME (GBM)          8       10        1
  OLIGOASTROCYTOMA                      33       43       38
  OLIGODENDROGLIOMA                     57       48       62
  TREATED PRIMARY GBM                    2        1        0
  UNTREATED PRIMARY (DE NOVO) GBM       80       93       37
[1] 6 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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     4                        19
  subtype2                                0     5                        20
  subtype3                                1     3                         6
          vv
clus       WHITE
  subtype1   208
  subtype2   222
  subtype3   148
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   4        5        3
  BLACK OR AFRICAN AMERICAN              19       20        6
  WHITE                                 208      222      148
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1  10 210
  subtype2  11 220
  subtype3   8 143
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  210
  subtype2   11  220
  subtype3    8  143
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10       11        8
  NOT HISPANIC OR LATINO      210      220      143
[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(9) Variable = MRNASEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1  82 166
  subtype2 148  40
  subtype3 187  39
subtype1 subtype2 subtype3 
     248      188      226 
subtype1 subtype2 subtype3 
     166       40       39 
$subtype1
TCGA-CS-6665 TCGA-DH-A66B TCGA-E1-A7YN TCGA-FG-A87N TCGA-06-5408 TCGA-06-5410 
       51.55        42.05        23.90        18.64        11.74         3.55 
TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 TCGA-06-5415 TCGA-06-5416 TCGA-06-5417 
        4.54         8.81         8.98         8.55         6.71         5.10 
TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 TCGA-12-1597 TCGA-12-3650 
        2.73         3.75         6.15         4.57        22.19        10.95 
TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 TCGA-14-0781 TCGA-14-0790 
       34.92        14.53        14.93         3.22         0.95        13.78 
TCGA-14-1034 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 TCGA-14-2554 TCGA-16-1045 
       15.95        17.85         7.63         7.17        17.49        29.03 
TCGA-19-1390 TCGA-19-1787 TCGA-19-2619 TCGA-19-2620 TCGA-19-2624 TCGA-19-2625 
       25.38        12.66         9.67         4.87         0.16         4.08 
TCGA-19-2629 TCGA-19-4065 TCGA-19-5960 TCGA-26-5132 TCGA-26-5135 TCGA-26-5136 
       24.23         7.04        14.96         9.40         8.88        18.97 
TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 TCGA-27-1837 
        5.06        16.60         9.86        40.54        21.30        14.04 
TCGA-27-2519 TCGA-27-2521 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 
       18.08        16.77        16.08         7.59         2.86        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2509 TCGA-32-1970 TCGA-32-1982 TCGA-32-2615 
        2.53         1.22         4.77        15.39         4.67        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
        8.84        22.78        25.18        19.86        19.23         0.85 
TCGA-41-2572 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 TCGA-76-4926 
       13.35        11.84         0.20        15.12         4.80         4.54 
TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-CS-4941 
       17.59         3.09         3.65         9.17        47.93         7.69 
TCGA-CS-6186 TCGA-CS-6188 TCGA-DH-5140 TCGA-DH-5142 TCGA-DU-5847 TCGA-DU-5852 
       17.69        26.76        19.96        63.88        18.02         6.74 
TCGA-DU-5854 TCGA-DU-6392 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 
        8.45       211.17         7.04        11.64       133.74        19.89 
TCGA-DU-6406 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 
       16.83        11.47        62.96        14.99         6.54         8.84 
TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TP TCGA-DU-A5TR 
       10.36         5.10        23.74        19.13        33.27        29.85 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TJ 
       24.43        26.17        33.96        26.76         7.50         0.56 
TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        29.13         3.65        19.46        12.43        16.18 
TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU 
       51.88        32.45        25.48        18.77        18.44        10.72 
TCGA-FG-A4MW TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7477 
       18.38        22.26        10.78         5.72        11.54        24.26 
TCGA-HT-7680 TCGA-HT-7686 TCGA-HT-7691 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 
        0.76        42.74         0.10         0.23         0.49         3.72 
TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8563 TCGA-HT-A4DS 
       16.24        12.23         0.10        13.78        28.27         0.23 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H 
       27.35         5.33        16.14        17.52        17.65         2.43 
TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A5F6 TCGA-P5-A72U TCGA-QH-A6CS 
       12.76        14.40         7.99         1.28         0.23        19.33 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6U0 TCGA-S9-A6UA 
       14.53        12.23         9.90        18.77        24.39         5.85 
TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R2 TCGA-S9-A7R7 
       85.55        19.86        26.47         7.92        10.39        98.63 
TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84J 
       20.48        54.77        24.92        16.18        28.08        24.16 
TCGA-TQ-A7RP TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VM-A8CF TCGA-VW-A8FI TCGA-02-0047 
       30.05        43.20         7.89        20.02         8.05        14.73 
TCGA-02-0055 TCGA-02-2483 TCGA-02-2485 TCGA-02-2486 TCGA-06-0125 TCGA-06-0129 
        2.50        15.32        15.45        20.32        47.61        33.67 
TCGA-06-0130 TCGA-06-0132 TCGA-06-0138 TCGA-06-0141 TCGA-06-0156 TCGA-06-0157 
       12.95        25.35        24.23        10.29         5.85         3.19 
TCGA-06-0158 TCGA-06-0168 TCGA-06-0174 TCGA-06-0178 TCGA-06-0184 TCGA-06-0187 
       10.82        19.66         3.22        88.14        69.90        27.22 
TCGA-06-0190 TCGA-06-0210 TCGA-06-0211 TCGA-06-0219 TCGA-06-0238 TCGA-06-0644 
       10.42         7.40        11.84         0.72        13.32        12.62 
TCGA-06-0645 TCGA-06-0646 TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 
        5.75         5.75         2.10        14.20        26.40        46.88 
TCGA-06-0745 TCGA-06-0747 TCGA-06-0749 TCGA-06-0750 TCGA-06-0878 TCGA-06-0882 
        7.86         2.70         2.70         0.92         7.17        20.78 
TCGA-06-1804 TCGA-06-2557 TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 
       13.61         1.08        12.49         4.93        17.65        12.56 
TCGA-06-2563 TCGA-06-2564 TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-06-2570 
       30.64         5.95        16.64         4.37         0.43        31.50 
TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 TCGA-12-0619 TCGA-12-0821 TCGA-14-0787 
       18.02        14.73        12.99        34.92        10.62         2.24 
TCGA-14-0789 TCGA-14-0817 TCGA-15-0742 TCGA-15-1444 TCGA-16-0846 TCGA-26-5133 
       11.24         5.39        13.78        50.53         3.91        14.86 
TCGA-26-5134 TCGA-26-5139 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 TCGA-28-5207 
        5.49         1.58         7.30         5.26        14.93        11.28 
TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 TCGA-28-5218 
       17.88        14.53        31.27        11.01        13.64         5.16 
TCGA-28-5220 TCGA-32-2616 
       12.76         7.36 

$subtype2
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A713 TCGA-IK-8125 
       46.88        46.72        62.01        20.09        20.45        42.77 
TCGA-R8-A73M TCGA-06-5411 TCGA-32-1980 TCGA-CS-5393 TCGA-CS-5395 TCGA-CS-5397 
       59.38         8.35         1.18        40.18        21.01         6.38 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5276 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5281 
       49.12       122.73        72.92        91.13        44.52        78.28 
TCGA-DB-A4XB TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64O 
       30.21        33.57        72.95        31.63        24.20        25.48 
TCGA-DB-A64R TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 
       31.40        14.40        18.51        11.24        16.18        46.06 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6400 TCGA-DU-6408 
       17.19        54.25        14.56        17.46         1.22       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7019 
        7.96         2.40       156.23       154.36       105.21        26.30 
TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 
        7.96        18.94        60.30        23.31         2.76        14.60 
TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 
       21.40        16.96        14.17        25.55        21.57        95.11 
TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC 
       22.29        11.41        21.30        17.98        51.52        37.38 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YM 
       44.42        38.89        79.99        57.93       134.27        21.30 
TCGA-E1-A7YO TCGA-E1-A7YU TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-F6-A8O3 
       75.02         0.76       146.14        13.08        73.48         0.23 
TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7638 TCGA-FG-7641 
        0.20        47.77        52.21        14.93        22.55        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8189 TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 
       20.09        28.34        22.52        16.44        36.66        48.69 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 
        0.10        40.11         3.75        17.42         6.54        75.19 
TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7608 
       95.93       172.77        23.18         4.57         3.16        22.06 
TCGA-HT-7610 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7690 TCGA-HT-7694 
       56.09        44.68         0.10        31.69         0.10         6.90 
TCGA-HT-7695 TCGA-HT-7854 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
       14.53        39.48        39.09        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 
        5.33        35.47        31.43         1.64         9.40         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 TCGA-HT-8113 
       37.87        33.01         6.25         0.46         5.56        29.59 
TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 
       13.74        15.72        26.04         0.13        20.22         0.07 
TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A TCGA-HT-A74J 
        0.10        16.93         1.81        16.83         6.38        10.52 
TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-A5KJ 
       45.44        41.49        69.27        35.44        39.75        31.63 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72X TCGA-P5-A731 
        2.37         9.44         7.96         7.59        13.25         9.01 
TCGA-P5-A733 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65Z 
       13.61         3.45         4.41        15.16        12.62        14.04 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC TCGA-QH-A86X TCGA-R8-A6MK 
       13.41         9.17         1.91        16.70        11.08        88.83 
TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WE 
        2.07        30.67        62.17        35.38        35.15       135.22 
TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       38.56        84.99        31.10        36.13        26.93        19.99 
TCGA-S9-A7J3 TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A89V TCGA-TM-A7C4 
       20.68        28.37        27.16       169.84        18.71        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84O TCGA-TM-A84R TCGA-TQ-A7RO TCGA-TQ-A7RQ 
       34.78        65.39        33.24        18.61        31.20        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-VM-A8CA TCGA-VM-A8CB TCGA-W9-A837 TCGA-WY-A859 
       25.87        61.41        13.51         0.10        51.06        39.88 
TCGA-WY-A85E TCGA-26-1442 
       20.81        31.33 

$subtype3
TCGA-DH-5141 TCGA-DU-A76O TCGA-FG-A60K TCGA-HT-A619 TCGA-HW-7490 TCGA-CS-4938 
       31.82        17.16        17.82        21.40        45.60       117.50 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6290 
       43.89        36.36        60.10         0.26        53.62        37.38 
TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 
       46.95        48.30        49.94        81.96        75.25        47.93 
TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XE 
       50.86        36.56        46.42        18.84        39.78        37.45 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K 
       30.12         5.98        27.45        27.81        29.23        12.10 
TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F 
       17.88        30.74        24.59        30.21        27.81        17.19 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 
       23.21        17.46        13.71        18.61        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 
      182.33        18.94        17.49        15.16        52.11        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       49.02        75.16        46.06        65.75        87.45        94.52 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 TCGA-DU-7301 
      117.40        90.77        30.67        94.32        44.02        25.91 
TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-A5TS TCGA-DU-A5TW TCGA-DU-A6S7 
       41.98        20.68        15.48        31.69        24.99        20.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 
      139.04        84.33        50.14        67.46        41.13        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YH TCGA-E1-A7YS TCGA-E1-A7YW TCGA-E1-A7Z4 
       95.57       130.78        93.21        15.32        36.82       145.05 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
       32.35        39.48        36.82        42.54        41.33        15.35 
TCGA-FG-7636 TCGA-FG-7637 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8186 TCGA-FG-8188 
       17.88        40.08        13.68        14.24        16.01        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L 
       32.61        38.27        18.71        23.70        14.76        21.53 
TCGA-FG-A6IZ TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 
       15.02        28.54        27.52         6.67         0.13         0.03 
TCGA-HT-7473 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 
       16.54         6.38        40.34       106.95         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 
       29.85       122.47        17.29        45.99        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7692 
       14.27         0.16        16.24         6.05        14.96         2.96 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7884 
       17.52        19.23        50.63        23.61         3.68        11.28 
TCGA-HT-8013 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-A614 TCGA-HT-A74K 
       63.55         2.50         0.23        34.19         2.70        15.35 
TCGA-HT-A74L TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8321 
       11.05         0.10        56.58        68.32        40.01        42.54 
TCGA-HW-8322 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A74X TCGA-P5-A5EV 
       24.92        28.87        20.71        19.00        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 
        6.71         2.30         5.88        10.42        11.64        10.95 
TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A65S 
        9.60         7.56        12.23        19.20         2.37         2.53 
TCGA-QH-A65X TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6X3 TCGA-QH-A6X4 TCGA-QH-A6X5 
       15.85        14.83        13.61        10.29        14.53        16.34 
TCGA-QH-A6X8 TCGA-QH-A6XA TCGA-QH-A870 TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X 
       16.73        16.50        12.99        94.03        32.65        30.87 
TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A845 TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX 
        5.46        28.08        19.59        87.12        41.10        40.93 
TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 
       36.82        25.81        29.85        32.61        98.24        95.93 
TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WO TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IY 
      123.65        75.25        18.61        18.64        14.07        23.51 
TCGA-S9-A7J0 TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R3 
       20.02         8.19         2.04        15.06        18.54        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A7C5 TCGA-TM-A84F TCGA-TM-A84G TCGA-TM-A84H 
       30.05        31.59        49.32        59.05        40.64        30.44 
TCGA-TM-A84L TCGA-TM-A84M TCGA-TM-A84Q TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       40.83        24.79        25.38        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM 
       19.69        15.98         2.04        40.41        44.09        36.69 
TCGA-TQ-A7RN TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-TQ-A8XE TCGA-VM-A8C8 TCGA-VM-A8CE 
       33.73        33.93        26.99        31.36        45.93        39.16 
TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WH-A86K TCGA-WY-A858 
       23.47        37.05        16.01        23.21        13.32        43.96 
TCGA-WY-A85A TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       43.40        45.80        46.88        37.71 

subtype1 subtype2 subtype3 
    0.10     0.07     0.03 
subtype1 subtype2 subtype3 
  211.17   172.77   182.33 
subtype1 subtype2 subtype3 
  13.335   22.535   26.450 
[1] "0.1 - 211.2 (13.3)" "0.1 - 172.8 (22.5)" "0.0 - 182.3 (26.4)"
D9V2, continuous
D9V3, binary
          cls
clus         0   1
  subtype1 149 101
  subtype2   3 187
  subtype3   0 227
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  149  101
  subtype2    3  187
  subtype3    0  227
                        clus
vv                       subtype1 subtype2 subtype3
  BRAIN                       149        3        0
  CENTRAL NERVOUS SYSTEM      101      187      227
[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"
D9V4, binary
          cls
clus         0   1
  subtype1 102 148
  subtype2  88 102
  subtype3  93 134
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  102  148
  subtype2   88  102
  subtype3   93  134
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      102       88       93
  MALE        148      102      134
[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"
D9V5, binary
          cls
clus         0   1
  subtype1  38 195
  subtype2  77 100
  subtype3  94 122
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38  195
  subtype2   77  100
  subtype3   94  122
     clus
vv    subtype1 subtype2 subtype3
  NO        38       77       94
  YES      195      100      122
[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"
D9V6, continuous
          vv
clus       ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA
  subtype1          72                             1               15
  subtype2          46                             0               45
  subtype3          76                             0               70
          vv
clus       OLIGODENDROGLIOMA TREATED PRIMARY GBM
  subtype1                14                   1
  subtype2                96                   0
  subtype3                81                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             147
  subtype2                               3
  subtype3                               0
D9V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  ASTROCYTOMA                           72       46       76
  GLIOBLASTOMA MULTIFORME (GBM)          1        0        0
  OLIGOASTROCYTOMA                      15       45       70
  OLIGODENDROGLIOMA                     14       96       81
  TREATED PRIMARY GBM                    1        0        0
  UNTREATED PRIMARY (DE NOVO) GBM      147        3        0
[1] 6 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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     7                        16
  subtype2                                0     3                         8
  subtype3                                0     3                         7
          vv
clus       WHITE
  subtype1   224
  subtype2   174
  subtype3   213
D9V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   7        3        3
  BLACK OR AFRICAN AMERICAN              16        8        7
  WHITE                                 224      174      213
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus         0   1
  subtype1   6 215
  subtype2  11 168
  subtype3  18 191
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  215
  subtype2   11  168
  subtype3   18  191
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6       11       18
  NOT HISPANIC OR LATINO      215      168      191
[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(10) Variable = MRNASEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  54 153
  subtype2 147  42
  subtype3 216  50
subtype1 subtype2 subtype3 
     207      189      266 
subtype1 subtype2 subtype3 
     153       42       50 
$subtype1
TCGA-E1-A7YN TCGA-06-5408 TCGA-06-5410 TCGA-06-5412 TCGA-06-5413 TCGA-06-5414 
       23.90        11.74         3.55         4.54         8.81         8.98 
TCGA-06-5415 TCGA-06-5416 TCGA-06-5418 TCGA-06-5856 TCGA-06-5858 TCGA-06-5859 
        8.55         6.71         2.73         3.75         6.15         4.57 
TCGA-12-1597 TCGA-12-3650 TCGA-12-3652 TCGA-12-3653 TCGA-12-5295 TCGA-12-5299 
       22.19        10.95        34.92        14.53        14.93         3.22 
TCGA-14-0781 TCGA-14-0790 TCGA-14-1034 TCGA-14-1823 TCGA-14-1825 TCGA-14-1829 
        0.95        13.78        15.95        17.85         7.63         7.17 
TCGA-14-2554 TCGA-16-1045 TCGA-19-1390 TCGA-19-1787 TCGA-19-2619 TCGA-19-2620 
       17.49        29.03        25.38        12.66         9.67         4.87 
TCGA-19-2624 TCGA-19-2625 TCGA-19-4065 TCGA-19-5960 TCGA-26-5132 TCGA-26-5135 
        0.16         4.08         7.04        14.96         9.40         8.88 
TCGA-26-5136 TCGA-27-1830 TCGA-27-1831 TCGA-27-1832 TCGA-27-1834 TCGA-27-1835 
       18.97         5.06        16.60         9.86        40.54        21.30 
TCGA-27-1837 TCGA-27-2519 TCGA-27-2523 TCGA-27-2524 TCGA-27-2526 TCGA-27-2528 
       14.04        18.08        16.08         7.59         2.86        15.78 
TCGA-28-1747 TCGA-28-1753 TCGA-28-2509 TCGA-32-1970 TCGA-32-1982 TCGA-32-2615 
        2.53         1.22         4.77        15.39         4.67        15.95 
TCGA-32-2632 TCGA-32-2634 TCGA-32-2638 TCGA-32-4213 TCGA-32-5222 TCGA-41-2571 
        8.84        22.78        25.18        19.86        19.23         0.85 
TCGA-41-2572 TCGA-41-3915 TCGA-41-4097 TCGA-41-5651 TCGA-76-4925 TCGA-76-4926 
       13.35        11.84         0.20        15.12         4.80         4.54 
TCGA-76-4927 TCGA-76-4928 TCGA-76-4929 TCGA-76-4931 TCGA-76-4932 TCGA-CS-4941 
       17.59         3.09         3.65         9.17        47.93         7.69 
TCGA-CS-6186 TCGA-CS-6188 TCGA-DB-A64O TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 
       17.69        26.76        25.48        18.02         6.74         8.45 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-7006 
        7.04        11.64       133.74        19.89        16.83        11.47 
TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 
        6.54         8.84        10.36         5.10        23.74        19.13 
TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-A7YD 
       24.43        33.96        26.76         7.50         0.56        14.30 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-FG-6688 TCGA-FG-6692 
       19.46        16.18        51.88        32.45        18.77        18.44 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7680 
       10.72        18.38        10.78         5.72        11.54         0.76 
TCGA-HT-7691 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 
        0.10         0.23         0.49         3.72        16.24        12.23 
TCGA-HT-8110 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C 
       13.78         0.23        27.35         5.33        16.14        17.65 
TCGA-HT-A74H TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A5F6 TCGA-P5-A72U TCGA-QH-A6CS 
        2.43        12.76        14.40         1.28         0.23        19.33 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7R2 
       14.53        12.23        24.39         5.85        19.86        10.39 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TQ-A7RP TCGA-VM-A8C9 TCGA-VM-A8CD 
       54.77        24.92        16.18        30.05        43.20         7.89 
TCGA-VW-A8FI TCGA-02-0047 TCGA-02-0055 TCGA-02-2485 TCGA-02-2486 TCGA-06-0125 
        8.05        14.73         2.50        15.45        20.32        47.61 
TCGA-06-0130 TCGA-06-0138 TCGA-06-0141 TCGA-06-0156 TCGA-06-0157 TCGA-06-0158 
       12.95        24.23        10.29         5.85         3.19        10.82 
TCGA-06-0168 TCGA-06-0174 TCGA-06-0184 TCGA-06-0187 TCGA-06-0190 TCGA-06-0210 
       19.66         3.22        69.90        27.22        10.42         7.40 
TCGA-06-0211 TCGA-06-0219 TCGA-06-0238 TCGA-06-0644 TCGA-06-0645 TCGA-06-0646 
       11.84         0.72        13.32        12.62         5.75         5.75 
TCGA-06-0649 TCGA-06-0686 TCGA-06-0743 TCGA-06-0744 TCGA-06-0745 TCGA-06-0747 
        2.10        14.20        26.40        46.88         7.86         2.70 
TCGA-06-0749 TCGA-06-0750 TCGA-06-0878 TCGA-06-0882 TCGA-06-1804 TCGA-06-2557 
        2.70         0.92         7.17        20.78        13.61         1.08 
TCGA-06-2558 TCGA-06-2559 TCGA-06-2561 TCGA-06-2562 TCGA-06-2563 TCGA-06-2564 
       12.49         4.93        17.65        12.56        30.64         5.95 
TCGA-06-2565 TCGA-06-2567 TCGA-06-2569 TCGA-08-0386 TCGA-12-0616 TCGA-12-0618 
       16.64         4.37         0.43        18.02        14.73        12.99 
TCGA-12-0619 TCGA-12-0821 TCGA-14-0787 TCGA-14-0789 TCGA-14-0817 TCGA-15-0742 
       34.92        10.62         2.24        11.24         5.39        13.78 
TCGA-16-0846 TCGA-26-5134 TCGA-26-5139 TCGA-28-2513 TCGA-28-2514 TCGA-28-5204 
        3.91         5.49         1.58         7.30         5.26        14.93 
TCGA-28-5207 TCGA-28-5208 TCGA-28-5209 TCGA-28-5213 TCGA-28-5215 TCGA-28-5216 
       11.28        17.88        14.53        31.27        11.01        13.64 
TCGA-28-5218 TCGA-28-5220 TCGA-32-2616 
        5.16        12.76         7.36 

$subtype2
TCGA-CS-6665 TCGA-DH-A66B TCGA-DU-A76O TCGA-FG-A87N TCGA-HW-7490 TCGA-06-5417 
       51.55        42.05        17.16        18.64        45.60         5.10 
TCGA-19-2629 TCGA-27-2521 TCGA-CS-4938 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 
       24.23        16.77       117.50        43.89        36.36        60.10 
TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5273 TCGA-DB-5275 TCGA-DB-5280 
       37.38        46.95        48.30        81.96        47.93        36.56 
TCGA-DB-A4XD TCGA-DB-A64S TCGA-DB-A75M TCGA-DB-A75O TCGA-DH-5140 TCGA-DH-5142 
       39.78        27.45        17.88        30.74        19.96        63.88 
TCGA-DH-A66D TCGA-DH-A7UT TCGA-DH-A7UU TCGA-DH-A7UV TCGA-DU-5853 TCGA-DU-5855 
       27.81        17.46        13.71        18.61        13.38         6.81 
TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6392 TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6399 
       18.94        17.49       211.17        49.02        75.16        65.75 
TCGA-DU-6401 TCGA-DU-6407 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7014 TCGA-DU-7015 
       87.45        94.52        62.96        14.99       117.40        90.77 
TCGA-DU-7019 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-8167 
       26.30        44.02        25.91        41.98        20.68        15.48 
TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A6S7 
       33.27        29.85        31.69        26.17        24.99        20.98 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5322 
      139.04        84.33        50.14        67.46        41.13       130.78 
TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YW TCGA-E1-A7Z4 
       29.13        93.21         3.65        12.43        36.82       145.05 
TCGA-E1-A7Z6 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-8182 
       32.35        25.48        36.82        42.54        41.33        13.68 
TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FG-A4MY 
       14.24        14.96        32.61        38.27        18.71        23.70 
TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-FN-7833 TCGA-HT-7472 
       14.76        21.53        22.26        28.54        27.52         0.03 
TCGA-HT-7473 TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 
       16.54        24.26         6.38        40.34       106.95         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
        5.03        29.85       122.47        17.29        22.06        45.99 
TCGA-HT-7611 TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7689 TCGA-HT-7693 
       57.60         0.16         6.05        42.74        14.96        17.52 
TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7902 
       39.48        19.23        50.63        23.61         3.68        31.43 
TCGA-HT-8013 TCGA-HT-8106 TCGA-HT-8108 TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 
       63.55         0.10         2.50         0.23        34.19        28.27 
TCGA-HT-A5R5 TCGA-HT-A614 TCGA-HT-A618 TCGA-HT-A61B TCGA-HT-A74O TCGA-HW-8320 
        0.13         2.70        16.83        17.52         0.10        40.01 
TCGA-HW-8321 TCGA-HW-A5KL TCGA-HW-A5KM TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW 
       42.54        28.87        20.71        19.00         0.23         6.71 
TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72W TCGA-P5-A72X TCGA-P5-A733 
        7.99         2.30         5.88        10.42        13.25        13.61 
TCGA-P5-A736 TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A6CU TCGA-QH-A6CW TCGA-QH-A6X3 
        7.56         2.37         2.53        14.83        13.61        10.29 
TCGA-QH-A870 TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U1 
       12.99         9.90        87.12        18.77        36.82        25.81 
TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A6WQ 
       98.24        95.93        85.55        26.47        18.61        14.07 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 
        7.92        23.51        20.02        18.54        99.06        30.05 
TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z TCGA-TM-A84F TCGA-TM-A84H TCGA-TM-A84I 
       98.63        31.59        20.48        59.05        30.44        28.08 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RH 
       24.16        40.83        25.38        23.80        21.37        15.98 
TCGA-TQ-A7RJ TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RR TCGA-TQ-A7RW TCGA-TQ-A8XE 
       40.41        44.09        36.69        25.87        26.99        31.36 
TCGA-VM-A8C8 TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 
       45.93        20.02        23.47        16.01        13.32        43.96 
TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D TCGA-02-2483 TCGA-06-0129 TCGA-06-0178 
       45.80        46.88        37.71        15.32        33.67        88.14 
TCGA-06-2570 TCGA-15-1444 TCGA-26-5133 
       31.50        50.53        14.86 

$subtype3
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DH-5141 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A60K 
       46.88        46.72        31.82        62.01        20.09        17.82 
TCGA-FG-A713 TCGA-HT-A619 TCGA-IK-8125 TCGA-R8-A73M TCGA-06-5411 TCGA-32-1980 
       20.45        21.40        42.77        59.38         8.35         1.18 
TCGA-CS-5393 TCGA-CS-5394 TCGA-CS-5395 TCGA-CS-5396 TCGA-CS-5397 TCGA-CS-6668 
       40.18         0.26        21.01        53.62         6.38        49.94 
TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5278 
       49.12       122.73        75.25        72.92        50.86        91.13 
TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XE 
       44.52        78.28        46.42        18.84        30.21        37.45 
TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64P TCGA-DB-A64Q 
       33.57        72.95        31.63        24.20        30.12         5.98 
TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A64W TCGA-DB-A64X TCGA-DB-A75K 
       31.40        27.81        29.23        14.40        18.51        12.10 
TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F 
       11.24        16.18        46.06        24.59        30.21        17.19 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5870 
       17.19        54.25        23.21        14.56        17.46       182.33 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6394 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-6408 
       15.16        52.11        22.42        46.06         1.22       114.08 
TCGA-DU-6410 TCGA-DU-6542 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7011 TCGA-DU-7018 
        7.96         2.40       156.23       154.36       105.21        30.67 
TCGA-DU-7292 TCGA-DU-7294 TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
        7.96        94.32        18.94        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A6S2 TCGA-DU-A6S3 
       14.60        21.40        16.96        14.17        25.55        21.57 
TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7TB 
       95.11        22.29        11.41        21.30        17.98        51.52 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 
       37.38        44.42        38.89        79.99        57.93       134.27 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YM TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU 
       78.21        95.57        21.30        75.02        15.32         0.76 
TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-F6-A8O4 
      146.14        13.08        73.48        39.48         0.23         0.20 
TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7634 TCGA-FG-7636 TCGA-FG-7637 
       47.77        52.21        14.93        15.35        17.88        40.08 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8189 
       22.55        20.61        20.09        28.34        16.01        22.52 
TCGA-FG-A6IZ TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 TCGA-HT-7467 TCGA-HT-7468 
       15.02        16.44        36.66        48.69         0.10         6.67 
TCGA-HT-7470 TCGA-HT-7471 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 
       40.11         0.13         3.75        17.42         6.54        75.19 
TCGA-HT-7481 TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 
       95.93       172.77        23.18         4.57         3.16        56.09 
TCGA-HT-7616 TCGA-HT-7620 TCGA-HT-7677 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 
        0.23        14.27        16.24        44.68         0.10        31.69 
TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 
        0.10         2.96         6.90        14.53        39.09        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-8010 
        0.33         0.13         5.33        35.47        11.28         1.64 
TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 
        9.40         0.10        37.87        33.01         6.25         0.46 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R7 
        5.56        29.59        13.74        15.72        26.04        20.22 
TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A61A TCGA-HT-A74J 
        0.07         0.10        16.93         1.81         6.38        10.52 
TCGA-HT-A74K TCGA-HT-A74L TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7491 
       15.35        11.05        56.58        45.44        41.49        68.32 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-8322 TCGA-HW-A5KJ TCGA-KT-A74X 
       69.27        35.44        39.75        24.92        31.63        14.40 
TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 TCGA-P5-A72Z TCGA-P5-A730 
        2.37         9.44         7.96         7.59        11.64        10.95 
TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A77W TCGA-P5-A77X TCGA-P5-A781 
        9.01         9.60        12.23        19.20         3.45         4.41 
TCGA-QH-A65R TCGA-QH-A65V TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6CY TCGA-QH-A6CZ 
       15.16        12.62        15.85        14.04        13.41         9.17 
TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       14.53        16.34        16.73         1.91        16.50        16.70 
TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y 
       11.08        88.83        94.03        32.65        30.87         5.46 
TCGA-RY-A840 TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TW 
       28.08         2.07        19.59        30.67        62.17        41.10 
TCGA-S9-A6TX TCGA-S9-A6TY TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U6 TCGA-S9-A6UB 
       40.93        35.38        29.85        32.61        35.15       123.65 
TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WP 
       75.25       135.22        38.56        84.99        31.10        18.64 
TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       36.13        26.93        19.99         8.19         2.04        20.68 
TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A89V TCGA-TM-A7C4 
       15.06        28.37        27.16       169.84        18.71        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O 
       49.32        34.78        65.39        40.64        24.79        33.24 
TCGA-TM-A84R TCGA-TM-A84S TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO 
       18.61        14.93        19.69         2.04        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-VM-A8CA TCGA-VM-A8CB TCGA-VM-A8CE 
       26.14        33.93        61.41        13.51         0.10        39.16 
TCGA-VV-A829 TCGA-VW-A7QS TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
       37.05        23.21        51.06        39.88        43.40        20.81 
TCGA-06-0132 TCGA-26-1442 
       25.35        31.33 

subtype1 subtype2 subtype3 
    0.10     0.03     0.07 
subtype1 subtype2 subtype3 
  133.74   211.17   182.33 
subtype1 subtype2 subtype3 
  11.740   26.300   22.865 
[1] "0.1 - 133.7 (11.7)" "0.0 - 211.2 (26.3)" "0.1 - 182.3 (22.9)"
D10V2, continuous
D10V3, binary
          cls
clus         0   1
  subtype1 139  69
  subtype2   9 181
  subtype3   4 265
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  139   69
  subtype2    9  181
  subtype3    4  265
                        clus
vv                       subtype1 subtype2 subtype3
  BRAIN                       139        9        4
  CENTRAL NERVOUS SYSTEM       69      181      265
[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"
D10V4, binary
          cls
clus         0   1
  subtype1  84 124
  subtype2  76 114
  subtype3 123 146
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84  124
  subtype2   76  114
  subtype3  123  146
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       84       76      123
  MALE        124      114      146
[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"
D10V5, binary
          cls
clus         0   1
  subtype1  34 158
  subtype2  49 130
  subtype3 126 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34  158
  subtype2   49  130
  subtype3  126  129
     clus
vv    subtype1 subtype2 subtype3
  NO        34       49      126
  YES      158      130      129
[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"
D10V6, continuous
          vv
clus       ASTROCYTOMA GLIOBLASTOMA MULTIFORME (GBM) OLIGOASTROCYTOMA
  subtype1          44                             0               13
  subtype2         100                             1               52
  subtype3          50                             0               65
          vv
clus       OLIGODENDROGLIOMA TREATED PRIMARY GBM
  subtype1                12                   1
  subtype2                29                   0
  subtype3               150                   0
          vv
clus       UNTREATED PRIMARY (DE NOVO) GBM
  subtype1                             138
  subtype2                               8
  subtype3                               4
D10V7, multiclass
                                 clus
vv                                subtype1 subtype2 subtype3
  ASTROCYTOMA                           44      100       50
  GLIOBLASTOMA MULTIFORME (GBM)          0        1        0
  OLIGOASTROCYTOMA                      13       52       65
  OLIGODENDROGLIOMA                     12       29      150
  TREATED PRIMARY GBM                    1        0        0
  UNTREATED PRIMARY (DE NOVO) GBM      138        8        4
[1] 6 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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                        16
  subtype2                                0     3                         7
  subtype3                                0     6                         8
          vv
clus       WHITE
  subtype1   185
  subtype2   178
  subtype3   248
D10V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   4        3        6
  BLACK OR AFRICAN AMERICAN              16        7        8
  WHITE                                 185      178      248
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus         0   1
  subtype1   6 174
  subtype2  12 165
  subtype3  17 235
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  174
  subtype2   12  165
  subtype3   17  235
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6       12       17
  NOT HISPANIC OR LATINO      174      165      235
[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(11) Variable = MIRSEQ_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 107  32
  subtype2  68  38
  subtype3  63  18
  subtype4 145  36
subtype1 subtype2 subtype3 subtype4 
     139      106       81      181 
subtype1 subtype2 subtype3 subtype4 
      32       38       18       36 
$subtype1
TCGA-DH-5141 TCGA-E1-A7YN TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4941 TCGA-CS-4942 
       31.82        23.90        45.60       117.50         7.69        43.89 
TCGA-CS-4944 TCGA-CS-5395 TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 
       60.10        21.01        17.69        37.38        46.95        48.30 
TCGA-DB-5274 TCGA-DB-5276 TCGA-DB-5280 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A64O 
       75.25        72.92        36.56        18.84        39.78        25.48 
TCGA-DB-A64V TCGA-DB-A75O TCGA-DH-A66F TCGA-DH-A7UV TCGA-DU-5847 TCGA-DU-5854 
       29.23        30.74        17.19        18.61        18.02         8.45 
TCGA-DU-5855 TCGA-DU-5872 TCGA-DU-6396 TCGA-DU-6407 TCGA-DU-6542 TCGA-DU-7012 
        6.81        17.49        75.16        94.52         2.40         6.54 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7290 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 
      117.40        90.77        10.36        25.91        41.98         5.10 
TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A6S7 
       23.74        19.13        24.43        24.99        33.96        20.98 
TCGA-E1-5318 TCGA-E1-5319 TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YJ TCGA-E1-A7YQ 
       78.21        95.57        14.30        93.21        19.46        51.88 
TCGA-E1-A7Z4 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7634 TCGA-FG-8182 TCGA-FG-8188 
      145.05        18.77        41.33        15.35        13.68        14.96 
TCGA-FG-8191 TCGA-FG-A4MT TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A70Y TCGA-FG-A87Q 
       32.61        38.27        23.70        21.53        28.54         5.72 
TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 TCGA-HT-7482 TCGA-HT-7485 
       27.52         0.03        16.54        40.34       106.95         4.01 
TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 TCGA-HT-7608 TCGA-HT-7609 
        5.03        29.85       122.47        17.29        22.06        45.99 
TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7689 TCGA-HT-7854 TCGA-HT-7855 TCGA-HT-7858 
       57.60         0.76        14.96        39.48        19.23        50.63 
TCGA-HT-7860 TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8110 TCGA-HT-8111 TCGA-HT-8563 
        0.49        16.24        63.55        13.78         0.23        28.27 
TCGA-HT-A4DS TCGA-HT-A617 TCGA-HT-A61C TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-8320 
        0.23        16.14        17.65        15.35         0.10        40.01 
TCGA-HW-A5KK TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F6 
       12.76         0.23         6.71         2.30         5.88         1.28 
TCGA-P5-A72W TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A735 TCGA-P5-A736 TCGA-QH-A65S 
       10.42        11.64        10.95         9.60         7.56         2.53 
TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A83X 
       19.33        14.83        14.53        10.29        12.99        30.87 
TCGA-RY-A840 TCGA-S9-A6TU TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6U8 
       28.08        87.12        40.93        29.85        32.61        98.24 
TCGA-S9-A6U9 TCGA-S9-A6WD TCGA-S9-A6WM TCGA-S9-A6WO TCGA-S9-A6WQ TCGA-S9-A7IY 
       95.93        75.25        19.86        18.61        14.07        23.51 
TCGA-S9-A7QX TCGA-S9-A7R2 TCGA-S9-A7R3 TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84O 
       18.54        10.39        99.06        31.59        24.92        33.24 
TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RP 
       14.93        23.80        21.37        44.09        36.69        30.05 
TCGA-TQ-A7RW TCGA-VM-A8CF TCGA-VV-A829 TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 
       26.99        20.02        37.05        16.01        13.32        43.96 
TCGA-WY-A85D 
       37.71 

$subtype2
TCGA-CS-6665 TCGA-DH-A66B TCGA-FG-A87N TCGA-HT-A619 TCGA-CS-4943 TCGA-CS-6188 
       51.55        42.05        18.64        21.40        36.36        26.76 
TCGA-DB-5273 TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A64S TCGA-DB-A64X TCGA-DH-5142 
       81.96        37.45        33.57        27.45        18.51        63.88 
TCGA-DH-A66D TCGA-DH-A66G TCGA-DH-A7UU TCGA-DU-6392 TCGA-DU-6399 TCGA-DU-6401 
       27.81        17.19        13.71       211.17        65.75        87.45 
TCGA-DU-6402 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6408 TCGA-DU-7006 
        7.04       133.74        19.89        16.83       114.08        11.47 
TCGA-DU-7007 TCGA-DU-7013 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TU TCGA-DU-A76L 
       62.96         8.84        33.27        29.85        26.17        26.76 
TCGA-DU-A7T8 TCGA-DU-A7TD TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 
      139.04         7.50         0.56        50.14        67.46        41.13 
TCGA-E1-5322 TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YV TCGA-E1-A7YW 
      130.78         3.65        12.43        16.18        32.45        36.82 
TCGA-FG-5963 TCGA-FG-6692 TCGA-FG-7636 TCGA-FG-8185 TCGA-FG-A4MU TCGA-FG-A4MX 
       25.48        18.44        17.88        14.24        10.72        18.71 
TCGA-FG-A60J TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-HT-7468 TCGA-HT-7469 TCGA-HT-7477 
       14.76        22.26        10.78         6.67        11.54        24.26 
TCGA-HT-7478 TCGA-HT-7676 TCGA-HT-7684 TCGA-HT-7686 TCGA-HT-7690 TCGA-HT-7691 
        6.38         0.16         6.05        42.74         0.10         0.10 
TCGA-HT-7693 TCGA-HT-7857 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 TCGA-HT-8106 
       17.52         0.23        23.61         3.68         3.72         0.10 
TCGA-HT-8114 TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-A5KL 
       34.19        27.35         5.33        16.83        17.52        28.87 
TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A72U TCGA-P5-A72X 
       20.71        19.00        14.40         7.99         0.23        13.25 
TCGA-QH-A6CX TCGA-RY-A845 TCGA-S9-A6TV TCGA-S9-A6TZ TCGA-S9-A6U0 TCGA-S9-A6U1 
       12.23        19.59        18.77        36.82        24.39        25.81 
TCGA-S9-A6UA TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7R4 TCGA-S9-A7R7 
        5.85        85.55        26.47         7.92        30.05        98.63 
TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84J 
       18.71        20.48        54.77        16.18        28.08        24.16 
TCGA-TM-A84L TCGA-TM-A84Q TCGA-TQ-A7RH TCGA-VM-A8C8 TCGA-VM-A8C9 TCGA-VM-A8CH 
       40.83        25.38        15.98        45.93        43.20        23.47 
TCGA-VW-A8FI TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85E 
        8.05        45.80        46.88        20.81 

$subtype3
TCGA-FG-A60K TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-5275 
       17.82        59.38         0.26        53.62        49.94        47.93 
TCGA-DB-5277 TCGA-DB-5279 TCGA-DB-A4X9 TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A75K 
       50.86        44.52        46.42        30.12         5.98        12.10 
TCGA-DH-5140 TCGA-DH-5144 TCGA-DH-A669 TCGA-DU-5870 TCGA-DU-5874 TCGA-DU-6393 
       19.96        24.59        30.21       182.33        15.16        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6400 TCGA-DU-7018 TCGA-DU-7294 
       22.42        49.02        46.06         1.22        30.67        94.32 
TCGA-DU-8168 TCGA-DU-A76R TCGA-DU-A7TA TCGA-E1-A7YE TCGA-E1-A7YO TCGA-E1-A7YS 
       14.17        21.30        84.33        29.13        75.02        15.32 
TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-6690 TCGA-FG-7637 TCGA-FG-A6IZ 
       32.35        39.48         0.23        42.54        40.08        15.02 
TCGA-FG-A6J1 TCGA-HT-7471 TCGA-HT-7483 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7692 
       16.44         0.13       172.77         0.23        16.24         2.96 
TCGA-HT-8012 TCGA-HT-A5R9 TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8322 TCGA-HW-A5KJ 
        9.40         0.07        11.05        68.32        24.92        31.63 
TCGA-KT-A74X TCGA-P5-A737 TCGA-P5-A77W TCGA-QH-A65R TCGA-QH-A65X TCGA-QH-A65Z 
       14.40        12.23        19.20        15.16        15.85        14.04 
TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83Y TCGA-RY-A83Z 
       16.73        11.08        94.03        32.65         5.46         9.90 
TCGA-S9-A6TW TCGA-S9-A6UB TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A7J0 TCGA-S9-A7J1 
       41.10       123.65       135.22        38.56        20.02         8.19 
TCGA-S9-A7J2 TCGA-S9-A7R1 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84M 
        2.04       169.84        49.32        40.64        30.44        24.79 
TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RU TCGA-TQ-A8XE 
       19.69         2.04        33.73        31.20        33.93        31.36 
TCGA-VM-A8CB TCGA-VM-A8CE TCGA-VW-A7QS 
        0.10        39.16        23.21 

$subtype4
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 TCGA-FG-A713 
       46.88        46.72        62.01        17.16        20.09        20.45 
TCGA-IK-8125 TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 
       42.77        40.18         6.38        49.12       122.73        91.13 
TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XG TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64R 
       78.28        30.21        72.95        31.63        24.20        31.40 
TCGA-DB-A64U TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 TCGA-DH-A7UR 
       27.81        14.40        11.24        16.18        46.06        54.25 
TCGA-DH-A7US TCGA-DH-A7UT TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5852 TCGA-DU-5853 
       23.21        17.46        14.56        17.46         6.74        13.38 
TCGA-DU-5871 TCGA-DU-6403 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 TCGA-DU-7010 
       18.94        11.64         7.96       156.23       154.36        14.99 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7299 TCGA-DU-7302 TCGA-DU-7304 
       26.30         7.96        18.94        44.02        60.30        23.31 
TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8163 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8167 
        2.76        14.60        20.68        21.40        16.96        15.48 
TCGA-DU-A5TS TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A76K 
       31.69        25.55        21.57        95.11        22.29        11.41 
TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5305 
       17.98        51.52        37.38        44.42        38.89        79.99 
TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YM TCGA-E1-A7YU TCGA-E1-A7YY TCGA-E1-A7Z2 
       57.93       134.27        21.30         0.76       146.14        13.08 
TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
       73.48         0.20        47.77        52.21        36.82        14.93 
TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8189 
       22.55        20.61        20.09        28.34        16.01        22.52 
TCGA-FG-A4MW TCGA-FG-A710 TCGA-FG-A711 TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 
       18.38        36.66        48.69         0.10        40.11         3.75 
TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 
       17.42         6.54        75.19        95.93        23.18         4.57 
TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 
        3.16        56.09        14.27        44.68         0.10        31.69 
TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 
        6.90        14.53        39.09        37.15         0.33         0.13 
TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8015 
        5.33        35.47        11.28        31.43         1.64         0.10 
TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8104 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 
       37.87        33.01        12.23         6.25         0.46         2.50 
TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV TCGA-HT-A5R5 
        5.56        29.59        13.74        15.72        26.04         0.13 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A616 TCGA-HT-A61A 
       20.22         0.10         2.70        16.93         1.81         6.38 
TCGA-HT-A74H TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 
        2.43        56.58        45.44        41.49        69.27        35.44 
TCGA-HW-8319 TCGA-HW-8321 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F2 TCGA-P5-A5F4 
       39.75        42.54         2.37         9.44         7.96         7.59 
TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A77X TCGA-P5-A780 TCGA-P5-A781 TCGA-QH-A65V 
        9.01        13.61         3.45         2.37         4.41        12.62 
TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X5 TCGA-QH-A6X9 TCGA-QH-A6XA 
       13.41         9.17        14.53        16.34         1.91        16.50 
TCGA-QH-A6XC TCGA-R8-A6MK TCGA-RY-A843 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TY 
       16.70        88.83         2.07        30.67        62.17        35.38 
TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WP TCGA-S9-A7IQ TCGA-S9-A7IX 
       35.15        84.99        31.10        18.64        36.13        26.93 
TCGA-S9-A7IZ TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C4 
       19.99        20.68        15.06        28.37        27.16        48.33 
TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84R TCGA-TQ-A7RJ TCGA-TQ-A7RQ 
       34.78        65.39        59.05        18.61        40.41        26.14 
TCGA-TQ-A7RR TCGA-TQ-A7RV TCGA-VM-A8CA TCGA-VM-A8CD TCGA-W9-A837 TCGA-WY-A859 
       25.87        61.41        13.51         7.89        51.06        39.88 
TCGA-WY-A85A 
       43.40 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.10     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 
  145.05   211.17   182.33   156.23 
subtype1 subtype2 subtype3 subtype4 
  23.510   21.105   24.920   21.400 
[1] "0.0 - 145.1 (23.5)" "0.1 - 211.2 (21.1)" "0.1 - 182.3 (24.9)"
[4] "0.1 - 156.2 (21.4)"
D11V2, continuous
D11V3, binary
          cls
clus         0
  subtype1 140
  subtype2 106
  subtype3  83
  subtype4 182
[1] "NOT AVAILABLE: table only has an event [0]"
D11V4, binary
          cls
clus        0  1
  subtype1 61 79
  subtype2 43 63
  subtype3 38 45
  subtype4 88 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   61   79
  subtype2   43   63
  subtype3   38   45
  subtype4   88   94
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       61       43       38       88
  MALE         79       63       45       94
[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"
D11V5, binary
          cls
clus        0  1
  subtype1 45 84
  subtype2 27 74
  subtype3 39 39
  subtype4 73 97
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   84
  subtype2   27   74
  subtype3   39   39
  subtype4   73   97
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        45       27       39       73
  YES       84       74       39       97
[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"
D11V6, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          69               35                36
  subtype2          66               22                18
  subtype3           5               20                58
  subtype4          53               50                79
D11V7, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             69       66        5       53
  OLIGOASTROCYTOMA        35       22       20       50
  OLIGODENDROGLIOMA       36       18       58       79
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        10
  subtype2                                0     2                         3
  subtype3                                0     3                         2
  subtype4                                0     2                         6
          vv
clus       WHITE
  subtype1   125
  subtype2   100
  subtype3    75
  subtype4   171
D11V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   1        2        3        2
  BLACK OR AFRICAN AMERICAN              10        3        2        6
  WHITE                                 125      100       75      171
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
          cls
clus         0   1
  subtype1   9 121
  subtype2   3  94
  subtype3   8  67
  subtype4  12 163
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  121
  subtype2    3   94
  subtype3    8   67
  subtype4   12  163
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            9        3        8       12
  NOT HISPANIC OR LATINO      121       94       67      163
[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(12) Variable = MIRSEQ_CHIERARCHICAL
D12V1, survival
          sevent
clus2        0   1
  subtype1 177  42
  subtype2 149  36
  subtype3  57  46
subtype1 subtype2 subtype3 
     219      185      103 
subtype1 subtype2 subtype3 
      42       36       46 
$subtype1
TCGA-DH-5141 TCGA-DH-A66B TCGA-FG-A60K TCGA-HT-A619 TCGA-HW-7490 TCGA-CS-4938 
       31.82        42.05        17.82        21.40        45.60       117.50 
TCGA-CS-4941 TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5394 TCGA-CS-5396 
        7.69        43.89        36.36        60.10         0.26        53.62 
TCGA-CS-6186 TCGA-CS-6290 TCGA-CS-6666 TCGA-CS-6667 TCGA-CS-6668 TCGA-DB-5273 
       17.69        37.38        46.95        48.30        49.94        81.96 
TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 TCGA-DB-5277 TCGA-DB-5280 TCGA-DB-A4X9 
       75.25        47.93        72.92        50.86        36.56        46.42 
TCGA-DB-A4XA TCGA-DB-A4XB TCGA-DB-A4XD TCGA-DB-A4XE TCGA-DB-A64P TCGA-DB-A64Q 
       18.84        30.21        39.78        37.45        30.12         5.98 
TCGA-DB-A64S TCGA-DB-A64U TCGA-DB-A64V TCGA-DB-A75K TCGA-DB-A75O TCGA-DH-5140 
       27.45        27.81        29.23        12.10        30.74        19.96 
TCGA-DH-5142 TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A66F TCGA-DH-A7UT 
       63.88        24.59        30.21        27.81        17.19        17.46 
TCGA-DH-A7UV TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-6394 
       18.61         6.81       182.33        18.94        17.49        22.42 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6407 
       49.02        75.16        46.06        65.75        87.45        94.52 
TCGA-DU-6408 TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-7299 
      114.08       117.40        90.77        30.67        94.32        44.02 
TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8163 TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A76R 
       25.91        41.98        20.68        24.99        20.98        21.30 
TCGA-DU-A7T8 TCGA-DU-A7TA TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 
      139.04        84.33        50.14        67.46        41.13        78.21 
TCGA-E1-5319 TCGA-E1-5322 TCGA-E1-A7YD TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YW 
       95.57       130.78        14.30        29.13        93.21        36.82 
TCGA-E1-A7Z4 TCGA-E1-A7Z6 TCGA-EZ-7264 TCGA-FG-6690 TCGA-FG-6691 TCGA-FG-7634 
      145.05        32.35        39.48        42.54        41.33        15.35 
TCGA-FG-7637 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FG-A4MT 
       40.08        13.68        14.24        14.96        32.61        38.27 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6IZ TCGA-FG-A70Y 
       18.71        23.70        14.76        21.53        15.02        28.54 
TCGA-FN-7833 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
       27.52         6.67         0.13         0.03        16.54        40.34 
TCGA-HT-7482 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7606 
      106.95         4.01         5.03        29.85       122.47        17.29 
TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 TCGA-HT-7676 TCGA-HT-7677 
       22.06        45.99        57.60         0.23         0.16        16.24 
TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7692 TCGA-HT-7693 
        0.76         6.05        14.96         0.10         2.96        17.52 
TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 TCGA-HT-8111 
       19.23        50.63        23.61         3.68        63.55         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A614 TCGA-HT-A74K TCGA-HT-A74L TCGA-HT-A74O 
       34.19        28.27         2.70        15.35        11.05         0.10 
TCGA-HW-7491 TCGA-HW-8320 TCGA-HW-8322 TCGA-HW-A5KL TCGA-KT-A74X TCGA-P5-A5EV 
       68.32        40.01        24.92        28.87        14.40         0.23 
TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A5F6 TCGA-P5-A72W 
        6.71         2.30         5.88         7.96         1.28        10.42 
TCGA-P5-A72Z TCGA-P5-A730 TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A736 TCGA-P5-A737 
       11.64        10.95         9.01         9.60         7.56        12.23 
TCGA-P5-A77W TCGA-P5-A780 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A65Z TCGA-QH-A6CS 
       19.20         2.37         2.53        12.62        14.04        19.33 
TCGA-QH-A6CU TCGA-QH-A6X3 TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-QH-A870 
       14.83        10.29        16.34        16.73        11.08        12.99 
TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-RY-A847 
       94.03        32.65        30.87         5.46        28.08        30.67 
TCGA-S9-A6TU TCGA-S9-A6TW TCGA-S9-A6TX TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6U2 
       87.12        41.10        40.93        36.82        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6U8 TCGA-S9-A6U9 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WO 
       32.61        98.24        95.93       123.65        75.25        18.61 
TCGA-S9-A6WP TCGA-S9-A6WQ TCGA-S9-A7IY TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 
       18.64        14.07        23.51         8.19         2.04        20.68 
TCGA-S9-A7QX TCGA-S9-A7R3 TCGA-S9-A7R4 TCGA-TM-A84B TCGA-TM-A84G TCGA-TM-A84H 
       18.54        99.06        30.05        24.92        40.64        30.44 
TCGA-TM-A84L TCGA-TM-A84O TCGA-TM-A84Q TCGA-TM-A84S TCGA-TM-A84T TCGA-TQ-A7RF 
       40.83        33.24        25.38        14.93        23.80        21.37 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-TQ-A7RN 
       19.69        15.98         2.04        44.09        36.69        33.73 
TCGA-TQ-A7RP TCGA-TQ-A7RR TCGA-TQ-A7RU TCGA-TQ-A7RW TCGA-VM-A8C8 TCGA-VM-A8CE 
       30.05        25.87        33.93        26.99        45.93        39.16 
TCGA-VM-A8CF TCGA-VM-A8CH TCGA-VV-A829 TCGA-VV-A86M TCGA-VW-A7QS TCGA-WH-A86K 
       20.02        23.47        37.05        16.01        23.21        13.32 
TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85D 
       43.96        45.80        37.71 

$subtype2
TCGA-CS-6670 TCGA-DB-A4XC TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 TCGA-FG-A713 
       46.88        46.72        62.01        17.16        20.09        20.45 
TCGA-IK-8125 TCGA-R8-A73M TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-DB-5270 
       42.77        59.38        40.18         6.38        49.12       122.73 
TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-5281 TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A4XH 
       91.13        44.52        78.28        33.57        72.95        31.63 
TCGA-DB-A64L TCGA-DB-A64R TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 
       24.20        31.40        14.40        11.24        16.18        46.06 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DH-A7US TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-5853 
       17.19        54.25        23.21        14.56        17.46        13.38 
TCGA-DU-5874 TCGA-DU-6393 TCGA-DU-6400 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7009 
       15.16        52.11         1.22         7.96       156.23       154.36 
TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 
       26.30         7.96        18.94        60.30        23.31         2.76 
TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 TCGA-DU-8168 TCGA-DU-A5TS TCGA-DU-A6S2 
       14.60        21.40        16.96        14.17        31.69        25.55 
TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A6S8 TCGA-DU-A7T6 TCGA-DU-A7TB TCGA-DU-A7TC 
       21.57        95.11        22.29        17.98        51.52        37.38 
TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YM 
       44.42        38.89        79.99        57.93       134.27        21.30 
TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YU TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 
       75.02        15.32         0.76       146.14        13.08        73.48 
TCGA-F6-A8O3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-6689 
        0.23         0.20        47.77        52.21        36.82        14.93 
TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 
       17.88        22.55        20.61        20.09        28.34        16.01 
TCGA-FG-8189 TCGA-FG-A6J1 TCGA-FG-A710 TCGA-FG-A711 TCGA-HT-7467 TCGA-HT-7470 
       22.52        16.44        36.66        48.69         0.10        40.11 
TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7477 TCGA-HT-7480 TCGA-HT-7481 
        3.75        17.42         6.54        24.26        75.19        95.93 
TCGA-HT-7483 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 
      172.77        23.18         4.57         3.16        56.09        14.27 
TCGA-HT-7681 TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 
       44.68         0.10        31.69         6.90        14.53        39.09 
TCGA-HT-7874 TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 
       37.15         0.33         0.13         5.33        35.47        11.28 
TCGA-HT-7902 TCGA-HT-8010 TCGA-HT-8012 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 
       31.43         1.64         9.40         0.10        37.87        33.01 
TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 
        6.25         0.46         2.50         5.56        29.59        13.74 
TCGA-HT-A4DV TCGA-HT-A5R5 TCGA-HT-A5R7 TCGA-HT-A5R9 TCGA-HT-A5RB TCGA-HT-A615 
       26.04         0.13        20.22         0.07         0.10        16.93 
TCGA-HT-A616 TCGA-HT-A618 TCGA-HT-A61A TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 
        1.81        16.83         6.38        56.58        45.44        41.49 
TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-A5KJ TCGA-P5-A5EY TCGA-P5-A5F0 
       69.27        35.44        39.75        31.63         2.37         9.44 
TCGA-P5-A5F4 TCGA-P5-A72X TCGA-P5-A733 TCGA-P5-A77X TCGA-P5-A781 TCGA-QH-A65R 
        7.59        13.25        13.61         3.45         4.41        15.16 
TCGA-QH-A65X TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X4 TCGA-QH-A6X9 TCGA-QH-A6XA 
       15.85        13.41         9.17        14.53         1.91        16.50 
TCGA-RY-A843 TCGA-RY-A845 TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WE 
        2.07        19.59        62.17        35.38        35.15       135.22 
TCGA-S9-A6WG TCGA-S9-A6WH TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX 
       85.55        38.56        84.99        31.10        36.13        26.93 
TCGA-S9-A7IZ TCGA-S9-A7QW TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-TM-A7C4 
       19.99        15.06        28.37        27.16       169.84        48.33 
TCGA-TM-A7C5 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F TCGA-TM-A84M TCGA-TM-A84R 
       49.32        34.78        65.39        59.05        24.79        18.61 
TCGA-TQ-A7RJ TCGA-TQ-A7RO TCGA-TQ-A7RQ TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8CA 
       40.41        31.20        26.14        61.41        31.36        13.51 
TCGA-VM-A8CB TCGA-VM-A8CD TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A 
        0.10         7.89        51.06        39.88        43.40 

$subtype3
TCGA-CS-6665 TCGA-E1-A7YN TCGA-FG-A87N TCGA-CS-5395 TCGA-CS-6188 TCGA-DB-A64O 
       51.55        23.90        18.64        21.01        26.76        25.48 
TCGA-DB-A64X TCGA-DH-A7UU TCGA-DU-5847 TCGA-DU-5852 TCGA-DU-5854 TCGA-DU-6392 
       18.51        13.71        18.02         6.74         8.45       211.17 
TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6542 
        7.04        11.64       133.74        19.89        16.83         2.40 
TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7010 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 
       11.47        62.96        14.99         6.54         8.84        10.36 
TCGA-DU-8158 TCGA-DU-8161 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A5TP TCGA-DU-A5TR 
        5.10        23.74        19.13        15.48        33.27        29.85 
TCGA-DU-A5TT TCGA-DU-A5TU TCGA-DU-A5TY TCGA-DU-A76K TCGA-DU-A76L TCGA-DU-A7TD 
       24.43        26.17        33.96        11.41        26.76         7.50 
TCGA-DU-A7TJ TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL TCGA-E1-A7YQ 
        0.56         3.65        19.46        12.43        16.18        51.88 
TCGA-E1-A7YV TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW 
       32.45        25.48        18.77        18.44        10.72        18.38 
TCGA-FG-A6J3 TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7469 TCGA-HT-7478 TCGA-HT-7686 
       22.26        10.78         5.72        11.54         6.38        42.74 
TCGA-HT-7691 TCGA-HT-7854 TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 
        0.10        39.48         0.23         0.49         3.72        16.24 
TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA 
       12.23         0.10        13.78        15.72         0.23        27.35 
TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61B TCGA-HT-A61C TCGA-HT-A74H TCGA-HW-8321 
        5.33        16.14        17.52        17.65         2.43        42.54 
TCGA-HW-A5KK TCGA-HW-A5KM TCGA-IK-7675 TCGA-KT-A7W1 TCGA-P5-A5EX TCGA-P5-A72U 
       12.76        20.71        19.00        14.40         7.99         0.23 
TCGA-QH-A6CV TCGA-QH-A6CX TCGA-QH-A6XC TCGA-R8-A6MK TCGA-RY-A83Z TCGA-S9-A6TV 
       14.53        12.23        16.70        88.83         9.90        18.77 
TCGA-S9-A6U0 TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A7IS TCGA-S9-A7J0 
       24.39         5.85        19.86        26.47         7.92        20.02 
TCGA-S9-A7R2 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89V TCGA-S9-A89Z TCGA-TM-A7C3 
       10.39        98.63        31.59        18.71        20.48        54.77 
TCGA-TM-A84C TCGA-TM-A84I TCGA-TM-A84J TCGA-VM-A8C9 TCGA-VW-A8FI TCGA-WY-A85C 
       16.18        28.08        24.16        43.20         8.05        46.88 
TCGA-WY-A85E 
       20.81 

subtype1 subtype2 subtype3 
    0.03     0.07     0.10 
subtype1 subtype2 subtype3 
  182.33   172.77   211.17 
subtype1 subtype2 subtype3 
   27.45    23.31    17.52 
[1] "0.0 - 182.3 (27.4)" "0.1 - 172.8 (23.3)" "0.1 - 211.2 (17.5)"
D12V2, continuous
D12V3, binary
          cls
clus         0
  subtype1 222
  subtype2 186
  subtype3 103
[1] "NOT AVAILABLE: table only has an event [0]"
D12V4, binary
          cls
clus         0   1
  subtype1  91 131
  subtype2  90  96
  subtype3  49  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91  131
  subtype2   90   96
  subtype3   49   54
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       91       90       49
  MALE        131       96       54
[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"
D12V5, binary
          cls
clus         0   1
  subtype1  91 119
  subtype2  76  97
  subtype3  17  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   91  119
  subtype2   76   97
  subtype3   17   78
     clus
vv    subtype1 subtype2 subtype3
  NO        91       76       17
  YES      119       97       78
[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"
D12V6, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          76               67                79
  subtype2          48               44                94
  subtype3          69               16                18
D12V7, multiclass
                   clus
vv                  subtype1 subtype2 subtype3
  ASTROCYTOMA             76       48       69
  OLIGOASTROCYTOMA        67       44       16
  OLIGODENDROGLIOMA       79       94       18
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                         7
  subtype2                                0     3                         8
  subtype3                                1     2                         6
          vv
clus       WHITE
  subtype1   208
  subtype2   170
  subtype3    93
D12V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        3        2
  BLACK OR AFRICAN AMERICAN               7        8        6
  WHITE                                 208      170       93
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
          cls
clus         0   1
  subtype1  17 188
  subtype2  12 164
  subtype3   3  93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17  188
  subtype2   12  164
  subtype3    3   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           17       12        3
  NOT HISPANIC OR LATINO      188      164       93
[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(13) Variable = MIRSEQ_MATURE_CNMF
D13V1, survival
          sevent
clus2        0   1
  subtype1  90  36
  subtype2  74  44
  subtype3  92  12
  subtype4 123  32
subtype1 subtype2 subtype3 subtype4 
     126      118      104      155 
subtype1 subtype2 subtype3 subtype4 
      36       44       12       32 
$subtype1
TCGA-CS-6665 TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-6186 TCGA-CS-6188 TCGA-CS-6290 
       51.55        45.60       117.50        17.69        26.76        37.38 
TCGA-CS-6666 TCGA-CS-6667 TCGA-DB-5279 TCGA-DB-A75O TCGA-DU-5847 TCGA-DU-5852 
       46.95        48.30        44.52        30.74        18.02         6.74 
TCGA-DU-5853 TCGA-DU-5854 TCGA-DU-5855 TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 
       13.38         8.45         6.81       182.33        18.94        17.49 
TCGA-DU-6395 TCGA-DU-6396 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6401 TCGA-DU-6402 
       49.02        75.16        46.06        65.75        87.45         7.04 
TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 TCGA-DU-6407 TCGA-DU-6408 
       11.64       133.74        19.89        16.83        94.52       114.08 
TCGA-DU-6542 TCGA-DU-7006 TCGA-DU-7007 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7014 
        2.40        11.47        62.96         6.54         8.84       117.40 
TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-8158 TCGA-DU-8161 
       90.77        44.02        25.91        41.98         5.10        23.74 
TCGA-DU-8163 TCGA-DU-8165 TCGA-DU-8167 TCGA-DU-A6S7 TCGA-E1-5305 TCGA-E1-5319 
       20.68        19.13        15.48        20.98        79.99        95.57 
TCGA-E1-A7Z6 TCGA-FG-5963 TCGA-FG-5965 TCGA-FG-6688 TCGA-FG-6691 TCGA-FG-7634 
       32.35        25.48        36.82        18.77        41.33        15.35 
TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 TCGA-FN-7833 TCGA-HT-7469 
       13.68        14.24        14.96        32.61        27.52        11.54 
TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 
        0.03        16.54       106.95       172.77         4.01         5.03 
TCGA-HT-7602 TCGA-HT-7604 TCGA-HT-7608 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7616 
       29.85       122.47        22.06        45.99        57.60         0.23 
TCGA-HT-7620 TCGA-HT-7676 TCGA-HT-7677 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7686 
       14.27         0.16        16.24         0.76         6.05        42.74 
TCGA-HT-7689 TCGA-HT-7690 TCGA-HT-7691 TCGA-HT-7693 TCGA-HT-7854 TCGA-HT-7855 
       14.96         0.10         0.10        17.52        39.48        19.23 
TCGA-HT-7857 TCGA-HT-7858 TCGA-HT-7860 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-7882 
        0.23        50.63         0.49        23.61         3.68         3.72 
TCGA-HT-8011 TCGA-HT-8013 TCGA-HT-8104 TCGA-HT-8106 TCGA-HT-8110 TCGA-HT-8111 
       16.24        63.55        12.23         0.10        13.78         0.23 
TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A74K TCGA-HT-A74O TCGA-HW-7486 TCGA-HW-8320 
       34.19        28.27        15.35         0.10        56.58        40.01 
TCGA-HW-8321 TCGA-IK-7675 TCGA-P5-A72W TCGA-P5-A730 TCGA-P5-A735 TCGA-P5-A780 
       42.54        19.00        10.42        10.95         9.60         2.37 
TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A83Z TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A7R3 
       10.29        12.99         9.90        87.12        36.82        99.06 
TCGA-S9-A89V TCGA-TM-A84I TCGA-TM-A84Q TCGA-TM-A84T TCGA-TQ-A7RF TCGA-TQ-A7RW 
       18.71        28.08        25.38        23.80        21.37        26.99 
TCGA-VM-A8C8 TCGA-VM-A8CH TCGA-WH-A86K TCGA-WY-A85B TCGA-WY-A85C TCGA-WY-A85D 
       45.93        23.47        13.32        45.80        46.88        37.71 

$subtype2
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-E1-A7YN TCGA-FG-A87N TCGA-CS-4941 
       46.72        31.82        42.05        23.90        18.64         7.69 
TCGA-CS-4942 TCGA-CS-4943 TCGA-CS-4944 TCGA-CS-5395 TCGA-DB-5273 TCGA-DB-5274 
       43.89        36.36        60.10        21.01        81.96        75.25 
TCGA-DB-5276 TCGA-DB-5281 TCGA-DB-A4XB TCGA-DB-A4XF TCGA-DB-A64O TCGA-DB-A64S 
       72.92        78.28        30.21        33.57        25.48        27.45 
TCGA-DB-A64V TCGA-DH-5140 TCGA-DH-5142 TCGA-DH-A669 TCGA-DH-A66D TCGA-DH-A7UT 
       29.23        19.96        63.88        30.21        27.81        17.46 
TCGA-DH-A7UV TCGA-DU-7290 TCGA-DU-A5TP TCGA-DU-A5TR TCGA-DU-A5TS TCGA-DU-A5TT 
       18.61        10.36        33.27        29.85        31.69        24.43 
TCGA-DU-A5TU TCGA-DU-A5TW TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7T8 TCGA-DU-A7TD 
       26.17        24.99        33.96        26.76       139.04         7.50 
TCGA-DU-A7TJ TCGA-E1-5302 TCGA-E1-5303 TCGA-E1-5304 TCGA-E1-5318 TCGA-E1-5322 
        0.56        50.14        67.46        41.13        78.21       130.78 
TCGA-E1-A7YD TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YJ TCGA-E1-A7YK TCGA-E1-A7YL 
       14.30        93.21         3.65        19.46        12.43        16.18 
TCGA-E1-A7YQ TCGA-E1-A7YV TCGA-E1-A7Z4 TCGA-FG-6692 TCGA-FG-A4MU TCGA-FG-A4MW 
       51.88        32.45       145.05        18.44        10.72        18.38 
TCGA-FG-A4MX TCGA-FG-A4MY TCGA-FG-A60J TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y 
       18.71        23.70        14.76        21.53        22.26        28.54 
TCGA-FG-A87Q TCGA-HT-7477 TCGA-HT-7479 TCGA-HT-A4DS TCGA-HT-A5R5 TCGA-HT-A5R9 
        5.72        24.26        40.34         0.23         0.13         0.07 
TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A614 TCGA-HT-A615 TCGA-HT-A617 TCGA-HT-A618 
       27.35         5.33         2.70        16.93        16.14        16.83 
TCGA-HT-A61B TCGA-HT-A61C TCGA-HW-A5KK TCGA-HW-A5KL TCGA-HW-A5KM TCGA-KT-A7W1 
       17.52        17.65        12.76        28.87        20.71        14.40 
TCGA-P5-A5EW TCGA-P5-A5EX TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A5F2 TCGA-P5-A72U 
        6.71         7.99         2.30         5.88         7.96         0.23 
TCGA-P5-A72X TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6CV 
       13.25         2.53        12.62        19.33        14.83        14.53 
TCGA-QH-A6CX TCGA-S9-A6TV TCGA-S9-A6TW TCGA-S9-A6U0 TCGA-S9-A6U8 TCGA-S9-A6UA 
       12.23        18.77        41.10        24.39        98.24         5.85 
TCGA-S9-A6WG TCGA-S9-A6WM TCGA-S9-A6WN TCGA-S9-A6WO TCGA-S9-A7IS TCGA-S9-A7IY 
       85.55        19.86        26.47        18.61         7.92        23.51 
TCGA-S9-A7J0 TCGA-S9-A7R2 TCGA-S9-A7R4 TCGA-S9-A7R7 TCGA-S9-A7R8 TCGA-S9-A89Z 
       20.02        10.39        30.05        98.63        31.59        20.48 
TCGA-TM-A7C3 TCGA-TM-A84B TCGA-TM-A84C TCGA-TQ-A7RK TCGA-TQ-A7RP TCGA-VM-A8C9 
       54.77        24.92        16.18        44.09        30.05        43.20 
TCGA-VM-A8CF TCGA-VV-A86M TCGA-VW-A8FI TCGA-WY-A858 
       20.02        16.01         8.05        43.96 

$subtype3
TCGA-FG-A60K TCGA-HT-A619 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 
       17.82        21.40        59.38         0.26        53.62        49.94 
TCGA-DB-5275 TCGA-DB-5277 TCGA-DB-A4X9 TCGA-DB-A4XA TCGA-DB-A4XD TCGA-DB-A4XG 
       47.93        50.86        46.42        18.84        39.78        72.95 
TCGA-DB-A64P TCGA-DB-A64Q TCGA-DB-A64R TCGA-DB-A64U TCGA-DB-A64X TCGA-DB-A75K 
       30.12         5.98        31.40        27.81        18.51        12.10 
TCGA-DH-5144 TCGA-DH-A66F TCGA-DH-A7US TCGA-DH-A7UU TCGA-DU-5874 TCGA-DU-6393 
       24.59        17.19        23.21        13.71        15.16        52.11 
TCGA-DU-6394 TCGA-DU-7008 TCGA-DU-7018 TCGA-DU-7294 TCGA-DU-8168 TCGA-DU-A6S8 
       22.42       156.23        30.67        94.32        14.17        22.29 
TCGA-DU-A76R TCGA-DU-A7TA TCGA-E1-A7YE TCGA-E1-A7YO TCGA-E1-A7YS TCGA-E1-A7YW 
       21.30        84.33        29.13        75.02        15.32        36.82 
TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-6690 TCGA-FG-7637 TCGA-FG-A4MT TCGA-FG-A6IZ 
       39.48         0.23        42.54        40.08        38.27        15.02 
TCGA-FG-A6J1 TCGA-FG-A710 TCGA-HT-7468 TCGA-HT-7471 TCGA-HT-7606 TCGA-HT-7692 
       16.44        36.66         6.67         0.13        17.29         2.96 
TCGA-HT-8012 TCGA-HT-A74L TCGA-HW-7491 TCGA-HW-8322 TCGA-KT-A74X TCGA-P5-A5EV 
        9.40        11.05        68.32        24.92        14.40         0.23 
TCGA-P5-A72Z TCGA-P5-A737 TCGA-P5-A77W TCGA-QH-A65X TCGA-QH-A65Z TCGA-QH-A6X4 
       11.64        12.23        19.20        15.85        14.04        14.53 
TCGA-QH-A6X5 TCGA-QH-A6X8 TCGA-QH-A86X TCGA-R8-A6MK TCGA-R8-A6ML TCGA-R8-A6MO 
       16.34        16.73        11.08        88.83        94.03        32.65 
TCGA-RY-A83X TCGA-RY-A83Y TCGA-RY-A840 TCGA-S9-A6TX TCGA-S9-A6U1 TCGA-S9-A6U2 
       30.87         5.46        28.08        40.93        25.81        29.85 
TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WP 
       32.61       123.65        75.25       135.22        38.56        18.64 
TCGA-S9-A7J1 TCGA-S9-A7J2 TCGA-S9-A7J3 TCGA-S9-A7QW TCGA-S9-A7QX TCGA-S9-A7R1 
        8.19         2.04        20.68        15.06        18.54       169.84 
TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84H TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S 
       49.32        40.64        30.44        24.79        33.24        14.93 
TCGA-TQ-A7RG TCGA-TQ-A7RH TCGA-TQ-A7RI TCGA-TQ-A7RM TCGA-TQ-A7RN TCGA-TQ-A7RO 
       19.69        15.98         2.04        36.69        33.73        31.20 
TCGA-TQ-A7RQ TCGA-TQ-A7RU TCGA-TQ-A7RV TCGA-TQ-A8XE TCGA-VM-A8CB TCGA-VM-A8CE 
       26.14        33.93        61.41        31.36         0.10        39.16 
TCGA-VV-A829 TCGA-VW-A7QS 
       37.05        23.21 

$subtype4
TCGA-CS-6670 TCGA-DU-7300 TCGA-DU-A76O TCGA-FG-8187 TCGA-FG-A713 TCGA-IK-8125 
       46.88        62.01        17.16        20.09        20.45        42.77 
TCGA-CS-5393 TCGA-CS-5397 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-5278 TCGA-DB-A4XE 
       40.18         6.38        49.12       122.73        91.13        37.45 
TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64W TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-5143 
       31.63        24.20        14.40        11.24        16.18        46.06 
TCGA-DH-A66G TCGA-DH-A7UR TCGA-DU-5849 TCGA-DU-5851 TCGA-DU-6392 TCGA-DU-6400 
       17.19        54.25        14.56        17.46       211.17         1.22 
TCGA-DU-6410 TCGA-DU-7009 TCGA-DU-7010 TCGA-DU-7019 TCGA-DU-7292 TCGA-DU-7298 
        7.96       154.36        14.99        26.30         7.96        18.94 
TCGA-DU-7302 TCGA-DU-7304 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 
       60.30        23.31         2.76        14.60        21.40        16.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A7T6 TCGA-DU-A7TB 
       25.55        21.57        95.11        11.41        17.98        51.52 
TCGA-DU-A7TC TCGA-DU-A7TG TCGA-DU-A7TI TCGA-E1-5307 TCGA-E1-5311 TCGA-E1-A7YM 
       37.38        44.42        38.89        57.93       134.27        21.30 
TCGA-E1-A7YU TCGA-E1-A7YY TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-5962 
        0.76       146.14        13.08        73.48         0.20        47.77 
TCGA-FG-5964 TCGA-FG-6689 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-7641 TCGA-FG-7643 
       52.21        14.93        17.88        22.55        20.61        20.09 
TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-A70Z TCGA-FG-A711 TCGA-HT-7467 
       28.34        16.01        22.52        10.78        48.69         0.10 
TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7478 TCGA-HT-7480 
       40.11         3.75        17.42         6.54         6.38        75.19 
TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7681 
       95.93        23.18         4.57         3.16        56.09        44.68 
TCGA-HT-7687 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 
        0.10        31.69         6.90        14.53        39.09        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7884 TCGA-HT-7902 
        0.33         0.13         5.33        35.47        11.28        31.43 
TCGA-HT-8010 TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 
        1.64         0.10        37.87        33.01         6.25         0.46 
TCGA-HT-8108 TCGA-HT-8109 TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-8564 TCGA-HT-A4DV 
        2.50         5.56        29.59        13.74        15.72        26.04 
TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A61A TCGA-HT-A74H TCGA-HW-7487 
       20.22         0.10         1.81         6.38         2.43        45.44 
TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 TCGA-HW-8319 TCGA-HW-A5KJ TCGA-P5-A5EY 
       41.49        69.27        35.44        39.75        31.63         2.37 
TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A731 TCGA-P5-A733 TCGA-P5-A77X TCGA-P5-A781 
        9.44         7.59         9.01        13.61         3.45         4.41 
TCGA-QH-A65R TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XA TCGA-QH-A6XC 
       15.16        13.41         9.17         1.91        16.50        16.70 
TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6TY TCGA-S9-A6U6 
        2.07        19.59        30.67        62.17        35.38        35.15 
TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A6WQ TCGA-S9-A7IQ TCGA-S9-A7IX TCGA-S9-A7IZ 
       84.99        31.10        14.07        36.13        26.93        19.99 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-TM-A7C4 TCGA-TM-A7CA TCGA-TM-A7CF TCGA-TM-A84F 
       28.37        27.16        48.33        34.78        65.39        59.05 
TCGA-TM-A84J TCGA-TM-A84L TCGA-TM-A84R TCGA-TQ-A7RJ TCGA-TQ-A7RR TCGA-VM-A8CA 
       24.16        40.83        18.61        40.41        25.87        13.51 
TCGA-VM-A8CD TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A TCGA-WY-A85E 
        7.89        51.06        39.88        43.40        20.81 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.07     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 
  182.33   145.05   169.84   211.17 
subtype1 subtype2 subtype3 subtype4 
  21.175   21.895   25.365   21.300 
[1] "0.0 - 182.3 (21.2)" "0.1 - 145.1 (21.9)" "0.1 - 169.8 (25.4)"
[4] "0.1 - 211.2 (21.3)"
D13V2, continuous
D13V3, binary
          cls
clus         0
  subtype1 126
  subtype2 119
  subtype3 106
  subtype4 156
[1] "NOT AVAILABLE: table only has an event [0]"
D13V4, binary
          cls
clus        0  1
  subtype1 53 73
  subtype2 49 70
  subtype3 50 56
  subtype4 77 79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   73
  subtype2   49   70
  subtype3   50   56
  subtype4   77   79
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       53       49       50       77
  MALE         73       70       56       79
[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"
D13V5, binary
          cls
clus        0  1
  subtype1 38 81
  subtype2 27 81
  subtype3 57 44
  subtype4 61 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   81
  subtype2   27   81
  subtype3   57   44
  subtype4   61   86
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        38       27       57       61
  YES       81       81       44       86
[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"
D13V6, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          58               36                32
  subtype2          74               23                22
  subtype3          13               26                67
  subtype4          46               41                69
D13V7, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4
  ASTROCYTOMA             58       74       13       46
  OLIGOASTROCYTOMA        36       23       26       41
  OLIGODENDROGLIOMA       32       22       67       69
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         5
  subtype2                                1     2                         7
  subtype3                                0     4                         3
  subtype4                                0     2                         6
          vv
clus       WHITE
  subtype1   119
  subtype2   107
  subtype3    95
  subtype4   146
D13V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                   0        2        4        2
  BLACK OR AFRICAN AMERICAN               5        7        3        6
  WHITE                                 119      107       95      146
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
          cls
clus         0   1
  subtype1   5 114
  subtype2   6 102
  subtype3  13  86
  subtype4   8 139
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  114
  subtype2    6  102
  subtype3   13   86
  subtype4    8  139
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        6       13        8
  NOT HISPANIC OR LATINO      114      102       86      139
[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(14) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D14V1, survival
          sevent
clus2       0  1
  subtype1 84 13
  subtype2 55 21
  subtype3 95 24
  subtype4 49  7
  subtype5 26 37
  subtype6 70 22
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      97       76      119       56       63       92 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      13       21       24        7       37       22 
$subtype1
TCGA-HW-7490 TCGA-CS-4938 TCGA-CS-4944 TCGA-CS-6186 TCGA-CS-6666 TCGA-CS-6667 
       45.60       117.50        60.10        17.69        46.95        48.30 
TCGA-DB-A4XD TCGA-DB-A64S TCGA-DB-A75O TCGA-DH-A7UV TCGA-DU-6396 TCGA-DU-6542 
       39.78        27.45        30.74        18.61        75.16         2.40 
TCGA-DU-7014 TCGA-DU-7015 TCGA-DU-7299 TCGA-DU-7301 TCGA-DU-7306 TCGA-DU-A5TP 
      117.40        90.77        44.02        25.91        41.98        33.27 
TCGA-DU-A5TW TCGA-DU-A6S7 TCGA-DU-A7TA TCGA-E1-5303 TCGA-E1-A7YD TCGA-E1-A7Z4 
       24.99        20.98        84.33        67.46        14.30       145.05 
TCGA-E1-A7Z6 TCGA-FG-6691 TCGA-FG-8182 TCGA-FG-8185 TCGA-FG-8188 TCGA-FG-8191 
       32.35        41.33        13.68        14.24        14.96        32.61 
TCGA-FG-A4MT TCGA-FG-A4MX TCGA-FN-7833 TCGA-HT-7472 TCGA-HT-7473 TCGA-HT-7479 
       38.27        18.71        27.52         0.03        16.54        40.34 
TCGA-HT-7482 TCGA-HT-7483 TCGA-HT-7485 TCGA-HT-7601 TCGA-HT-7602 TCGA-HT-7604 
      106.95       172.77         4.01         5.03        29.85       122.47 
TCGA-HT-7606 TCGA-HT-7609 TCGA-HT-7611 TCGA-HT-7680 TCGA-HT-7684 TCGA-HT-7689 
       17.29        45.99        57.60         0.76         6.05        14.96 
TCGA-HT-7693 TCGA-HT-7855 TCGA-HT-7858 TCGA-HT-7873 TCGA-HT-7879 TCGA-HT-8013 
       17.52        19.23        50.63        23.61         3.68        63.55 
TCGA-HT-8111 TCGA-HT-8114 TCGA-HT-8563 TCGA-HT-A74O TCGA-HW-A5KL TCGA-HW-A5KM 
        0.23        34.19        28.27         0.10        28.87        20.71 
TCGA-IK-7675 TCGA-P5-A5EV TCGA-P5-A5EW TCGA-P5-A5EZ TCGA-P5-A5F1 TCGA-P5-A72W 
       19.00         0.23         6.71         2.30         5.88        10.42 
TCGA-P5-A72X TCGA-P5-A72Z TCGA-P5-A730 TCGA-QH-A6X3 TCGA-QH-A870 TCGA-RY-A840 
       13.25        11.64        10.95        10.29        12.99        28.08 
TCGA-S9-A6TU TCGA-S9-A6TZ TCGA-S9-A6U1 TCGA-S9-A6WO TCGA-S9-A7QX TCGA-S9-A7R3 
       87.12        36.82        25.81        18.61        18.54        99.06 
TCGA-S9-A7R4 TCGA-S9-A7R8 TCGA-TM-A84B TCGA-TM-A84H TCGA-TM-A84Q TCGA-TM-A84T 
       30.05        31.59        24.92        30.44        25.38        23.80 
TCGA-TQ-A7RF TCGA-TQ-A7RK TCGA-TQ-A7RM TCGA-VM-A8C8 TCGA-VM-A8CF TCGA-VM-A8CH 
       21.37        44.09        36.69        45.93        20.02        23.47 
TCGA-VV-A829 TCGA-VV-A86M TCGA-WH-A86K TCGA-WY-A858 TCGA-WY-A85B TCGA-WY-A85C 
       37.05        16.01        13.32        43.96        45.80        46.88 
TCGA-WY-A85D 
       37.71 

$subtype2
TCGA-DB-A4XC TCGA-DH-5141 TCGA-DH-A66B TCGA-FG-A60K TCGA-FG-A87N TCGA-CS-4941 
       46.72        31.82        42.05        17.82        18.64         7.69 
TCGA-CS-4942 TCGA-CS-4943 TCGA-DB-5273 TCGA-DB-5274 TCGA-DB-5275 TCGA-DB-5276 
       43.89        36.36        81.96        75.25        47.93        72.92 
TCGA-DB-5277 TCGA-DB-5281 TCGA-DB-A4XA TCGA-DB-A64U TCGA-DB-A64V TCGA-DH-5140 
       50.86        78.28        18.84        27.81        29.23        19.96 
TCGA-DH-5142 TCGA-DH-A66D TCGA-DH-A7US TCGA-DH-A7UT TCGA-DU-7007 TCGA-DU-A5TR 
       63.88        27.81        23.21        17.46        62.96        29.85 
TCGA-DU-A5TS TCGA-DU-A5TU TCGA-E1-5302 TCGA-E1-5304 TCGA-E1-5311 TCGA-E1-5318 
       31.69        26.17        50.14        41.13       134.27        78.21 
TCGA-E1-5322 TCGA-E1-A7YE TCGA-E1-A7YH TCGA-E1-A7YI TCGA-E1-A7YK TCGA-E1-A7YV 
      130.78        29.13        93.21         3.65        12.43        32.45 
TCGA-FG-6690 TCGA-FG-A4MY TCGA-FG-A60L TCGA-FG-A6J3 TCGA-FG-A70Y TCGA-HT-7469 
       42.54        23.70        21.53        22.26        28.54        11.54 
TCGA-HT-7477 TCGA-HT-7478 TCGA-HT-7608 TCGA-HT-7686 TCGA-HT-8106 TCGA-HT-A4DV 
       24.26         6.38        22.06        42.74         0.10        26.04 
TCGA-HT-A5R9 TCGA-HT-A615 TCGA-HT-A618 TCGA-HT-A61B TCGA-HW-A5KJ TCGA-P5-A5EX 
        0.07        16.93        16.83        17.52        31.63         7.99 
TCGA-P5-A5F2 TCGA-QH-A65S TCGA-QH-A65V TCGA-QH-A6CS TCGA-QH-A6CU TCGA-QH-A6X5 
        7.96         2.53        12.62        19.33        14.83        16.34 
TCGA-R8-A6MK TCGA-RY-A83Z TCGA-S9-A6TV TCGA-S9-A6WG TCGA-S9-A6WN TCGA-S9-A6WQ 
       88.83         9.90        18.77        85.55        26.47        14.07 
TCGA-S9-A7IS TCGA-S9-A7IY TCGA-S9-A7J0 TCGA-S9-A7R7 TCGA-S9-A89Z TCGA-TM-A84I 
        7.92        23.51        20.02        98.63        20.48        28.08 
TCGA-TM-A84J TCGA-TQ-A7RR TCGA-TQ-A7RW TCGA-VW-A7QS 
       24.16        25.87        26.99        23.21 

$subtype3
TCGA-CS-6670 TCGA-DU-7300 TCGA-FG-8187 TCGA-FG-A713 TCGA-IK-8125 TCGA-CS-5393 
       46.88        62.01        20.09        20.45        42.77        40.18 
TCGA-CS-5397 TCGA-CS-6669 TCGA-DB-5270 TCGA-DB-A4XH TCGA-DB-A64L TCGA-DB-A64W 
        6.38        49.12       122.73        31.63        24.20        14.40 
TCGA-DB-A75L TCGA-DB-A75P TCGA-DH-A7UR TCGA-DU-5851 TCGA-DU-7009 TCGA-DU-7292 
       11.24        16.18        54.25        17.46       154.36         7.96 
TCGA-DU-7298 TCGA-DU-7302 TCGA-DU-7309 TCGA-DU-8162 TCGA-DU-8164 TCGA-DU-8166 
       18.94        60.30         2.76        14.60        21.40        16.96 
TCGA-DU-A6S2 TCGA-DU-A6S3 TCGA-DU-A6S6 TCGA-DU-A76K TCGA-DU-A7TB TCGA-DU-A7TC 
       25.55        21.57        95.11        11.41        51.52        37.38 
TCGA-DU-A7TG TCGA-E1-5305 TCGA-E1-5307 TCGA-E1-A7YM TCGA-E1-A7YU TCGA-E1-A7YY 
       44.42        79.99        57.93        21.30         0.76       146.14 
TCGA-E1-A7Z2 TCGA-E1-A7Z3 TCGA-F6-A8O4 TCGA-FG-5962 TCGA-FG-6689 TCGA-FG-7641 
       13.08        73.48         0.20        47.77        14.93        20.61 
TCGA-FG-7643 TCGA-FG-8181 TCGA-FG-8186 TCGA-FG-8189 TCGA-FG-A6J1 TCGA-FG-A711 
       20.09        28.34        16.01        22.52        16.44        48.69 
TCGA-HT-7467 TCGA-HT-7470 TCGA-HT-7474 TCGA-HT-7475 TCGA-HT-7476 TCGA-HT-7480 
        0.10        40.11         3.75        17.42         6.54        75.19 
TCGA-HT-7481 TCGA-HT-7603 TCGA-HT-7605 TCGA-HT-7607 TCGA-HT-7610 TCGA-HT-7620 
       95.93        23.18         4.57         3.16        56.09        14.27 
TCGA-HT-7681 TCGA-HT-7688 TCGA-HT-7694 TCGA-HT-7695 TCGA-HT-7856 TCGA-HT-7874 
       44.68        31.69         6.90        14.53        39.09        37.15 
TCGA-HT-7875 TCGA-HT-7877 TCGA-HT-7880 TCGA-HT-7881 TCGA-HT-7902 TCGA-HT-8010 
        0.33         0.13         5.33        35.47        31.43         1.64 
TCGA-HT-8015 TCGA-HT-8018 TCGA-HT-8019 TCGA-HT-8105 TCGA-HT-8107 TCGA-HT-8109 
        0.10        37.87        33.01         6.25         0.46         5.56 
TCGA-HT-8113 TCGA-HT-8558 TCGA-HT-A5R7 TCGA-HT-A5RB TCGA-HT-A616 TCGA-HT-A61A 
       29.59        13.74        20.22         0.10         1.81         6.38 
TCGA-HT-A74H TCGA-HW-7486 TCGA-HW-7487 TCGA-HW-7489 TCGA-HW-7493 TCGA-HW-7495 
        2.43        56.58        45.44        41.49        69.27        35.44 
TCGA-HW-8319 TCGA-P5-A5EY TCGA-P5-A5F0 TCGA-P5-A5F4 TCGA-P5-A733 TCGA-P5-A77X 
       39.75         2.37         9.44         7.59        13.61         3.45 
TCGA-P5-A781 TCGA-QH-A65R TCGA-QH-A6CY TCGA-QH-A6CZ TCGA-QH-A6X9 TCGA-QH-A6XC 
        4.41        15.16        13.41         9.17         1.91        16.70 
TCGA-S9-A6TY TCGA-S9-A6U6 TCGA-S9-A6WI TCGA-S9-A6WL TCGA-S9-A7IQ TCGA-S9-A7IX 
       35.38        35.15        84.99        31.10        36.13        26.93 
TCGA-S9-A7QY TCGA-S9-A7QZ TCGA-S9-A7R1 TCGA-S9-A89V TCGA-TM-A7C4 TCGA-TM-A7CF 
       28.37        27.16       169.84        18.71        48.33        65.39 
TCGA-TM-A84F TCGA-TM-A84R TCGA-W9-A837 TCGA-WY-A859 TCGA-WY-A85A 
       59.05        18.61        51.06        39.88        43.40 

$subtype4
TCGA-HT-A619 TCGA-R8-A73M TCGA-CS-5394 TCGA-CS-5396 TCGA-CS-6668 TCGA-DB-A64P 
       21.40        59.38         0.26        53.62        49.94        30.12 
TCGA-DB-A64Q TCGA-DB-A75K TCGA-DH-5144 TCGA-DH-A669 TCGA-DH-A66F TCGA-DU-7018 
        5.98        12.10        24.59        30.21        17.19        30.67 
TCGA-E1-5319 TCGA-E1-A7YS TCGA-EZ-7264 TCGA-F6-A8O3 TCGA-FG-7634 TCGA-FG-7637 
       95.57        15.32        39.48         0.23        15.35        40.08 
TCGA-FG-A6IZ TCGA-HT-7468 TCGA-HT-7616 TCGA-HT-7677 TCGA-HT-7692 TCGA-HT-A74K 
       15.02         6.67         0.23        16.24         2.96        15.35 
TCGA-HT-A74L TCGA-HW-7491 TCGA-KT-A74X TCGA-P5-A77W TCGA-QH-A65X TCGA-QH-A6X8 
       11.05        68.32        14.40        19.20        15.85        16.73 
TCGA-QH-A86X TCGA-R8-A6ML TCGA-R8-A6MO TCGA-RY-A83X TCGA-RY-A83Y TCGA-S9-A6TW 
       11.08        94.03        32.65        30.87         5.46        41.10 
TCGA-S9-A6TX TCGA-S9-A6U2 TCGA-S9-A6U5 TCGA-S9-A6UB TCGA-S9-A6WD TCGA-S9-A7J1 
       40.93        29.85        32.61       123.65        75.25         8.19 
TCGA-S9-A7J2 TCGA-TM-A7C5 TCGA-TM-A84G TCGA-TM-A84M TCGA-TM-A84O TCGA-TM-A84S 
        2.04        49.32        40.64        24.79        33.24        14.93 
TCGA-TQ-A7RG TCGA-TQ-A7RI TCGA-TQ-A7RN TCGA-TQ-A7RO TCGA-TQ-A7RU TCGA-TQ-A8XE 
       19.69         2.04        33.73        31.20        33.93        31.36 
TCGA-VM-A8CB TCGA-VM-A8CE 
        0.10        39.16 

$subtype5
TCGA-E1-A7YN TCGA-CS-5395 TCGA-CS-6188 TCGA-DB-A64O TCGA-DU-5847 TCGA-DU-5852 
       23.90        21.01        26.76        25.48        18.02         6.74 
TCGA-DU-5854 TCGA-DU-6402 TCGA-DU-6403 TCGA-DU-6404 TCGA-DU-6405 TCGA-DU-6406 
        8.45         7.04        11.64       133.74        19.89        16.83 
TCGA-DU-7006 TCGA-DU-7012 TCGA-DU-7013 TCGA-DU-7290 TCGA-DU-8158 TCGA-DU-8161 
       11.47         6.54         8.84        10.36         5.10        23.74 
TCGA-DU-8165 TCGA-DU-A5TT TCGA-DU-A5TY TCGA-DU-A76L TCGA-DU-A7TD TCGA-DU-A7TJ 
       19.13        24.43        33.96        26.76         7.50         0.56 
TCGA-E1-A7YJ TCGA-E1-A7YL TCGA-E1-A7YQ TCGA-FG-5963 TCGA-FG-6688 TCGA-FG-6692 
       19.46        16.18        51.88        25.48        18.77        18.44 
TCGA-FG-A4MU TCGA-FG-A4MW TCGA-FG-A70Z TCGA-FG-A87Q TCGA-HT-7691 TCGA-HT-7854 
       10.72        18.38        10.78         5.72         0.10        39.48 
TCGA-HT-7857 TCGA-HT-7860 TCGA-HT-7882 TCGA-HT-8011 TCGA-HT-8104 TCGA-HT-8110 
        0.23         0.49         3.72        16.24        12.23        13.78 
TCGA-HT-8564 TCGA-HT-A4DS TCGA-HT-A5RA TCGA-HT-A5RC TCGA-HT-A617 TCGA-HT-A61C 
       15.72         0.23        27.35         5.33        16.14        17.65 
TCGA-HW-A5KK TCGA-KT-A7W1 TCGA-P5-A72U TCGA-QH-A6CV TCGA-QH-A6CX TCGA-S9-A6U0 
       12.76        14.40         0.23        14.53        12.23        24.39 
TCGA-S9-A6UA TCGA-S9-A6WM TCGA-S9-A7R2 TCGA-TM-A7C3 TCGA-TM-A84C TCGA-TQ-A7RP 
        5.85        19.86        10.39        54.77        16.18        30.05 
TCGA-VM-A8C9 TCGA-VM-A8CD TCGA-VW-A8FI 
       43.20         7.89         8.05 

$subtype6
TCGA-CS-6665 TCGA-DU-A76O TCGA-CS-6290 TCGA-DB-5278 TCGA-DB-5279 TCGA-DB-A4X9 
       51.55        17.16        37.38        91.13        44.52        46.42 
TCGA-DB-A4XB TCGA-DB-A4XE TCGA-DB-A4XF TCGA-DB-A4XG TCGA-DB-A64R TCGA-DB-A64X 
       30.21        37.45        33.57        72.95        31.40        18.51 
TCGA-DH-5143 TCGA-DH-A66G TCGA-DH-A7UU TCGA-DU-5849 TCGA-DU-5853 TCGA-DU-5855 
       46.06        17.19        13.71        14.56        13.38         6.81 
TCGA-DU-5870 TCGA-DU-5871 TCGA-DU-5872 TCGA-DU-5874 TCGA-DU-6392 TCGA-DU-6393 
      182.33        18.94        17.49        15.16       211.17        52.11 
TCGA-DU-6394 TCGA-DU-6395 TCGA-DU-6397 TCGA-DU-6399 TCGA-DU-6400 TCGA-DU-6401 
       22.42        49.02        46.06        65.75         1.22        87.45 
TCGA-DU-6407 TCGA-DU-6408 TCGA-DU-6410 TCGA-DU-7008 TCGA-DU-7010 TCGA-DU-7019 
       94.52       114.08         7.96       156.23        14.99        26.30 
TCGA-DU-7294 TCGA-DU-7304 TCGA-DU-8163 TCGA-DU-8167 TCGA-DU-8168 TCGA-DU-A6S8 
       94.32        23.31        20.68        15.48        14.17        22.29 
TCGA-DU-A76R TCGA-DU-A7T6 TCGA-DU-A7T8 TCGA-DU-A7TI TCGA-E1-A7YO TCGA-E1-A7YW 
       21.30        17.98       139.04        38.89        75.02        36.82 
TCGA-FG-5964 TCGA-FG-5965 TCGA-FG-7636 TCGA-FG-7638 TCGA-FG-A60J TCGA-FG-A710 
       52.21        36.82        17.88        22.55        14.76        36.66 
TCGA-HT-7471 TCGA-HT-7676 TCGA-HT-7687 TCGA-HT-7690 TCGA-HT-7884 TCGA-HT-8012 
        0.13         0.16         0.10         0.10        11.28         9.40 
TCGA-HT-8108 TCGA-HT-A5R5 TCGA-HT-A614 TCGA-HW-8320 TCGA-HW-8321 TCGA-HW-8322 
        2.50         0.13         2.70        40.01        42.54        24.92 
TCGA-P5-A731 TCGA-P5-A735 TCGA-P5-A737 TCGA-P5-A780 TCGA-QH-A65Z TCGA-QH-A6X4 
        9.01         9.60        12.23         2.37        14.04        14.53 
TCGA-QH-A6XA TCGA-RY-A843 TCGA-RY-A845 TCGA-RY-A847 TCGA-S9-A6TS TCGA-S9-A6U8 
       16.50         2.07        19.59        30.67        62.17        98.24 
TCGA-S9-A6WE TCGA-S9-A6WH TCGA-S9-A6WP TCGA-S9-A7IZ TCGA-S9-A7J3 TCGA-S9-A7QW 
      135.22        38.56        18.64        19.99        20.68        15.06 
TCGA-TM-A7CA TCGA-TM-A84L TCGA-TQ-A7RH TCGA-TQ-A7RJ TCGA-TQ-A7RQ TCGA-TQ-A7RV 
       34.78        40.83        15.98        40.41        26.14        61.41 
TCGA-VM-A8CA TCGA-WY-A85E 
       13.51        20.81 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     0.07     0.10     0.10     0.10     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  172.77   134.27   169.84   123.65   133.74   211.17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  27.450   25.955   21.570   24.690   15.720   22.355 
[1] "0.0 - 172.8 (27.4)" "0.1 - 134.3 (26.0)" "0.1 - 169.8 (21.6)"
[4] "0.1 - 123.7 (24.7)" "0.1 - 133.7 (15.7)" "0.1 - 211.2 (22.4)"
D14V2, continuous
D14V3, binary
          cls
clus         0
  subtype1  98
  subtype2  77
  subtype3 120
  subtype4  57
  subtype5  63
  subtype6  92
[1] "NOT AVAILABLE: table only has an event [0]"
D14V4, binary
          cls
clus        0  1
  subtype1 34 64
  subtype2 36 41
  subtype3 59 61
  subtype4 23 34
  subtype5 31 32
  subtype6 46 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   64
  subtype2   36   41
  subtype3   59   61
  subtype4   23   34
  subtype5   31   32
  subtype6   46   46
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       34       36       59       23       31       46
  MALE         64       41       61       34       32       46
[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"
D14V5, binary
          cls
clus        0  1
  subtype1 34 58
  subtype2 19 55
  subtype3 47 66
  subtype4 37 17
  subtype5 11 45
  subtype6 35 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   58
  subtype2   19   55
  subtype3   47   66
  subtype4   37   17
  subtype5   11   45
  subtype6   35   51
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        34       19       47       37       11       35
  YES       58       55       66       17       45       51
[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"
D14V6, continuous
          vv
clus       ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
  subtype1          55               27                16
  subtype2          35               20                22
  subtype3          35               28                57
  subtype4           2               11                44
  subtype5          41               11                11
  subtype6          23               29                40
D14V7, multiclass
                   clus
vv                  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ASTROCYTOMA             55       35       35        2       41       23
  OLIGOASTROCYTOMA        27       20       28       11       11       29
  OLIGODENDROGLIOMA       16       22       57       44       11       40
[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"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         2
  subtype2                                0     2                         3
  subtype3                                0     2                         5
  subtype4                                0     3                         2
  subtype5                                1     1                         7
  subtype6                                0     0                         2
          vv
clus       WHITE
  subtype1    94
  subtype2    72
  subtype3   112
  subtype4    50
  subtype5    53
  subtype6    86
D14V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                   0        2        2        3        1
  BLACK OR AFRICAN AMERICAN               2        3        5        2        7
  WHITE                                  94       72      112       50       53
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        0
  ASIAN                                   0
  BLACK OR AFRICAN AMERICAN               2
  WHITE                                  86
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
          cls
clus         0   1
  subtype1   6  81
  subtype2   4  69
  subtype3   5 110
  subtype4   8  44
  subtype5   3  55
  subtype6   6  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   81
  subtype2    4   69
  subtype3    5  110
  subtype4    8   44
  subtype5    3   55
  subtype6    6   82
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        4        5        8        3        6
  NOT HISPANIC OR LATINO       81       69      110       44       55       82
[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"
